From manuel.holtgrewe@fu-berlin.de Thu Jan 05 16:25:54 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RipCS-0006w8-Ne>; Thu, 05 Jan 2012 16:25:52 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1RipCS-0001jO-LU>; Thu, 05 Jan 2012 16:25:52 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RipCS-0001bS-J5>; Thu, 05 Jan 2012 16:25:52 +0100 Message-ID: <4F05C0C6.5010106@fu-berlin.de> Date: Thu, 05 Jan 2012 16:24:54 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: SeqAn Development Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Originating-IP: 160.45.111.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1325777152-000067B8-AF8AD34C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001363, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: [Seqan-dev] [ANNOUNCE] External contribution: Availability of alf X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 05 Jan 2012 15:25:54 -0000 Dear all, I am happy to announce the availability of Jonathan Göke's alignment free comparison code in the SeqAn repository. There is an application called alf that allows the comparison of sequences based on word properties which is available from the SeqAn homepage: http://www.seqan.de/projects/alf.html The driving code behind this application is available as the SeqAn module alignment_free in extras. The full documentation of this module is available in the current trunk API documentation, for example see: http://docs.seqan.de/seqan/dev2/?i=Class.AFScore This marks the first external contribution of a whole module and app to SeqAn. We hope that its success will serve as a role model for future contributions. If one of you wants to contribute sequence analysis code to SeqAn then do not hesitate to contact us! Best Regards, Manuel From fheeger@mi.fu-berlin.de Fri Jan 06 14:35:42 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rj9xM-0006fj-Fi>; Fri, 06 Jan 2012 14:35:40 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rj9xM-0007OJ-Co>; Fri, 06 Jan 2012 14:35:40 +0100 Received: from bgbm6.bgbm.fu-berlin.de ([160.45.63.17] helo=[192.168.1.143]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1Rj9xM-0003Mi-8o>; Fri, 06 Jan 2012 14:35:40 +0100 From: Felix Heeger To: SeqAn Development In-Reply-To: <4EF217E3.1000605@fu-berlin.de> References: <1324484150.19199.29.camel@IR0912.bgbm.fu-berlin.de> <4EF217E3.1000605@fu-berlin.de> Content-Type: multipart/mixed; boundary="=-P56L6PDj2qGMqH8Kq7fJ" Date: Fri, 06 Jan 2012 14:35:36 +0100 Message-ID: <1325856936.20283.5.camel@IR0912.bgbm.fu-berlin.de> Mime-Version: 1.0 X-Mailer: Evolution 2.32.2 X-Originating-IP: 160.45.63.17 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1325856940-000067B8-EAACAB6A/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.074848, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.6 required=5.0 tests=ALL_TRUSTED,UPPERCASE_25_50 Subject: Re: [Seqan-dev] CheckStreamFormat for FastQ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 06 Jan 2012 13:35:42 -0000 --=-P56L6PDj2qGMqH8Kq7fJ Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit Hi Manual, thank you for your effort. I checked your suggestion today and it did not fix my problem. Also your example program can not identify my FASTQ file. I am pretty sure it is valid FASTQ as other programs work fine on it. I attached the first part of the file, if you want to have a look at it. felix On Wed, 2011-12-21 at 18:31 +0100, Manuel Holtgrewe wrote: > Felix, > > The documentation of checkStreamFormat() was misleading. I fixed it in > [10948]. > > http://docs.seqan.de/seqan/dev2/?i=Function.checkStreamFormat > > (The documentation is regenerated every hour, so you might wait for a > bit to see it). > > The following is a simple example program I compiled and tested. Please > write another email, if the problem persists. > > HTH, > Manuel > > #include > #include > > #include > #include > > int main(int argc, char ** argv) > { > using namespace seqan; > > if (argc != 2) > return 1; > std::fstream in(argv[1]); > > RecordReader > reader(in); > AutoSeqStreamFormat tagSelector; > bool b = checkStreamFormat(reader, tagSelector); > if (!b) > { > std::cerr << "Could not detect file format!" << std::endl; > return 1; > } > > // b is true if any format was detected successfully. > if (tagSelector.tagId == 1) > std::cerr << "Detected FASTA." << std::endl; > else if (tagSelector.tagId == 2) > std::cerr << "Detected FASTQ." << std::endl; > else > std::cerr << "Unknown file format!" << std::endl; > return 0; > } > > > On 12/21/2011 05:15 PM, Felix Heeger wrote: > > Hi, > > > > I have to different functions I want to call depending on the fact if a > > input file is fasta or fastq format. > > > > My approach to this is: > > > >> RecordReader > reader(inFile); > >> if (checkStreamFormat(reader, Fasta())) > >> { > >> std::cerr<< "Input file format is fasta."<< std::endl; > >> [call function for fasta] > >> } > >> else if (checkStreamFormat(reader, Fastq())) > >> { > >> std::cerr<< "Input file format is fastq."<< std::endl; > >> [call function for fastq] > >> } > >> else > >> { > >> std::cerr<< "ERORR: Input file format is not fasta or fastq."<< std::endl; > >> return -1; > >> } > > > > This works fine for fasta. However my fastq file is not recognized. > > I looked into the code for checkStreamFormat a bit and the file is not > > recognized because the iterator in the readRecord function reaches > > atEnd before the quality meta data for the 35th record is finished (l. 392). > > This happens with two different fastq files. > > > > So my theory is the following: > > In the checkStreamFormat function LimitRecordReaderInScope > > is used. The documentation states that this prevents the stream from > > "rebuffering". This probably prevents the reader from finishing to read > > the complete record and the recognition of the file fails. > > > > I hope I could make myself clear. I can also provide my code and a sample > > fastq file if it would be helpful. > > > > Cheers, > > felix > > > > > > > > _______________________________________________ > > seqan-dev mailing list > > seqan-dev@lists.fu-berlin.de > > https://lists.fu-berlin.de/listinfo/seqan-dev > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --=-P56L6PDj2qGMqH8Kq7fJ Content-Disposition: attachment; filename="lane_5_p1.fastq" Content-Type: text/plain; name="lane_5_p1.fastq"; charset="UTF-8" Content-Transfer-Encoding: 7bit @DHCDZDN1:106:5:2203:1124:1021#0/1 CGCCCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAACTTAGTGCGGACACCCGATCGGCATAGCGCACTACAGC + b__eeeeegggeghf_eghfiifgfeeghifhhfghiiiiegg\bceeedadddcdcccc\accbbcbcccaZac`accccccccRXb`ba[acc_b`bc @DHCDZDN1:106:5:2203:1134:1060#0/1 CTCTTGAATTCATGTCCTCTTCTCTATTCCCATGGCCACTGTCTTAGTTGAGGACTTCATCTTCTCTTATTTGGACTACTGTCATGGCCTTCTTTCTGGG + _bbeeeccgggggiiiiiiiiiiiiiiiiiifhiiiihiiigghihiiiighiOWafghiiiiiiiiiiiiihfg_fgiihhgegeggeeeeedddcbbb @DHCDZDN1:106:5:2203:1175:1067#0/1 TCCGAGTGTTGTGGATTAGGTTAACGATCGTCTCGTTCCCCTTTTGGTATTCGTTGCACAAGTATTGGGCCAGGAAAATGAGCAGTTCCCGTCCAACAGC + abbececcgggggihiiiiigghhhihhhihfhhiiiiiiihiiiiieghiiihiii`ghigbdeggedeebbc`accbccccccbccccc`acc]bccc @DHCDZDN1:106:5:2203:1136:1093#0/1 CCCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTGATGCCGAACTTAGTGCGGACACCCGATCGGCATAGCGCACTACAGCCCA + b__eeeeefggeghhhhhhegf[beghfhcghghhdhegfddgggdegededeeddccc_accb`bbc\]_accc_]aacaccacbcccca]bbbccca[ @DHCDZDN1:106:5:2203:1191:1105#0/1 CGGGCGCACATTGCCAGGGTACCTCAGACCCCTGAGCTCCGTGCAGATGTCTGTGTCCAGCCCTGGGCCCCCAGCCCCTCATCTGCATGAGAACTTGGGG + bbbeeeeegggggiiiiiiegiiiiiiiiiiiiigiiiiiibgghiiiihiihggegfggeeeedcccaccaccccccacccbbccG]_bcbcccccaaa @DHCDZDN1:106:5:2203:1115:1107#0/1 CTCTGCTGGGGGTAGGCACTTCGCACAGGGTACACAGCGGTCTGGTAGGGGTTGGGGGAGGAGGAGTATGGTGGCACTGCCCCGCTGGTGGGGGGACAGG + bbbeeeeegggg_fgigfiiiiiiiiiiiiefgfhhiiiiaghgg^dgeeeX`accccT_aW^a^_X^bcc`bc[^`bc]bacccaccJ[^cccEHOWW^ @DHCDZDN1:106:5:2203:1149:1112#0/1 CACGCCCCCACGGGATACAGCAGTGATAAAAATTAAGCCATGAACGAAAGTTCGACTAAGCTATGTTGATTAAGGGTTGGTTAATTTCGTGCCAGCCACC + b__eeeeegggggighfhfghffcefhhiiifiihfhiiifgdfgfeffdbgfhgfgeeeecbddcddbcc`bccc``acacccdccbb`aacbcccc_W @DHCDZDN1:106:5:2203:1152:1131#0/1 CCTCCCAACACAGCTTTCCGCTTCAGCGGACCCGTCCCGTCCTGATCCCGCGGCCGCCATGGTGCACGACTGTCCACACACCCACGCAGGCTCACCCATG + _^^^cc]cecg^e^[eaeYefUef]a`[Y^eg_ee\eeW\_[Z_ZbdZ`\[`]WWVTTVa`^JYSYSWWaa]`b]_`_^W[_]WQX_EX[]^_]`BBBBB @DHCDZDN1:106:5:2203:1148:1148#0/1 CGGGAGGACGACGGGGCGGACGTCGTGTGCTCTGTGAACCATGAGTCTCTAAAGGGGGCTGACAGGTCGACCTCTCAGCGCATCGAAGTCCTGTACACAC + abbeeecegggggiiighgeecaccZ_^acbcbbbbcccccbcbbbbbcc`bccccaccccccbc_Y`aacccbbb`bcccL[aab]^^bbbcbcbbbba @DHCDZDN1:106:5:2203:1074:1161#0/1 CGCGGCAGCACAGCGCCGGGCAGCTCTGCCGCCTGCAAGATGTCGCCAGCCCTCTGAAGCTTCATCGGACAGAGACTTTTCCTGCCTACCGATCCGAGCA + bbbeeeeegggeghiiiiiihhiiiiihiihhgdegceeeedddcccaccccccccccccccccddbc_aaabb[^]bcc]b]``a]_bcRTX[^[[_aX @DHCDZDN1:106:5:2203:1243:1169#0/1 AAATAGGTTTGGGGAAGTGGATAAGAGTTAACTTTAAAAGGAAATGTCAATCAGGCACTGCATACATTAATCTAGGATTCAGGCAAGGGTTCAAGCTCGA + ^__eeeecgggggifffdghghhiiggdghhiiihiiihiiiihhhghiiiiiihhhiiiiiiiiiiiiiiiggggfgeeeeeecdcccGZ`cbbccccc @DHCDZDN1:106:5:2203:1218:1199#0/1 CGCAGGTACTTGAGAACGTACAGGGGCAGACAGCTGACCAGAGTGATAACAGAGACCTTCCACAAGAACGACAAAGTGGCGATGAAGTACACATCGAGAT + bbbeeecegggggiiiiigfhiiiiiihighihiiiiiiiiih^bghihhiihihiihiigggggeeeeccccccb`bccccaabbcYY__bbbbabaa^ @DHCDZDN1:106:5:2203:1185:1220#0/1 CTCCGGGAAATGGCAGATGCAAAGAGCAAGGGGGTGCAGGTGTGCACACCTGCTCAGCGATATGGGATGTGGGGACAGACTTCACTCAGTTTTCATCCCA + bbbeeeeeggggcghifhiifgiihihihhhiiiV`gghighhggfgeeeeeddddddcaccccccbbabbccca]aabcccbbbccccbcdcbbccccb @DHCDZDN1:106:5:2203:1218:1246#0/1 ACCGCCTCTTCACGGGAAGGTCAATTTCACTGATTGGAAGTAAGAGACAGTTAAACCCTCGTGTGGCCTTTCATACAAGTCCTTAATTAGAGAACAAATG + ^aaeeeeegggggiiighhifgiiiiiiiiiifhiiifggfghhiihihgghiiiiiiiiicgggeeeeedddddbdbcbccccccdddcccbbc^bccb @DHCDZDN1:106:5:2203:1194:1248#0/1 CGAGAAATATACCCCACCAGCAAGAAAGTAAGCAGGGATGTTTGCTGCTTCAACTGCAGCTGAGGCCCAAGGCGGCTAGGAGACAGTTGTAAGTATTCGG + _b_eccceeggggiidgffhiiihghiifhfhhggiiefggfhhfhdhiiiiiiiiihhihichhfgggdeeecccaccc]bW^bb]b_]`b_]abcbc^ @DHCDZDN1:106:5:2203:1393:1024#0/1 GTCTGCAGGGCACGGCAGGGTGTGCAACAATTAATAATTTTTCTCCATTTCCACTGAGATCATACCTCCTTGTAGAAAGTATCTGTTCCTTACTCATCTG + ___cccccggggghhhhhhhXcYaeffffhhhfhfhfhhhhhhhhhhhhhhhefghhhhcggeggdddddbbbbbdbbb``abbccbbbbbbbbbbbbbb @DHCDZDN1:106:5:2203:1428:1052#0/1 ATGGACCCACATTTTCATTGGTGGTTCCACTGGGCAAACTAAACATGTAGCATAGAGTCATGGGCATGCTGGCGTTAGGATGGCCGTGGCATAGTTAGCG + ^__eceeeegcgghhhfhhhheeghhhh_fffhhhacafghddfeghhfghhhhh_efffhhhhfbgdgfeggec]]abbb`_bbc\\^a^__bcbb_ba @DHCDZDN1:106:5:2203:1406:1061#0/1 CTCACCGCTCCATGTGCGTCCCTCCCGAAGCTGCGCGCTCGGTCGAAGAGGACGACCTTCCCCGATAGAGGAGGACCGTTCTTCGGTCAAGGGTATACGA + bbbeeeeegggggiiihiigfhiiiiiiiiifgfghiiiige^c`^acccc_ac\YacccccccaZWabcaacc_ac_X[^acccc_]]b`b^GX_`ca[ @DHCDZDN1:106:5:2203:1354:1064#0/1 GAGCAACCCAAAGGTTATGAATCTCATCAGTAAATTGTCAGCCAAGTTTGGAGGTCAAGCATAATGCCCTTCTGACAAATAAAGCCCTTGCTGAAGGAAA + bbbeeeeegggggifgiiiiiiiiihiiiiiiiiiiighiiiighifgiiiiiieghiiihiiihifhiiiiigfggggeeeeeedcddccccccccccc @DHCDZDN1:106:5:2203:1394:1084#0/1 CTTGCGGCTGCCGTGCGCGGGCACAGGTTTGCCCTTCCCGTAGTATCCCGTGAAGATGGCCCTGACCTCCAGCTTCTTGGCCAGGCTCAGCAGCCCGCGC + ___cccccggae^[b_d_cgh[U__\bM^dZV^c^b`bb[UZ^KZZ_bbTKZW^_]R_bX^aW[bbb_`^^`bbbYY_GY]bX[_BBBBBBBBBBBBBBB @DHCDZDN1:106:5:2203:1261:1093#0/1 GCCATGGCCACATCCGGGCTGAACCGCATGGCTGTCTCGATGCCCGACTCCTGCTCAAAGTAGCCCGAGCCCGACCCTGAATAGAGGTTATCCAGCTCAT + ___cccccgegcgghY[degfffhhhhdcgdffffddddb]eegfhhheggdddddc]`bZ`bbbb]W^_\^aaaa]^^^bb`bbbaY^bbbbRR]Y]_` @DHCDZDN1:106:5:2203:1428:1104#0/1 GCTTGCTGATCAGTGGTAAGATTACATTGCAAGTAATGAGTTCCACCACTACATGGCGCCCAGTCCGGGTCTCCAAGTGGGGCTTTGGCACTAGTCCTTG + bbbeeeeeegggghiihhhiiiihifhiiihgighiiiiiiiiichiiiihigiiiiiiiiiiiiiigggeeeddddddccccccccccccccccccccc @DHCDZDN1:106:5:2203:1339:1107#0/1 GTAGAGCTCACTGGGAAAAAAATGCACACATTGCCATGTCCACATATATGCTTACAGTTTCAGCAGGAATGTGTGGGGCACCTACCACGTGCCAGACCCA + aaaeeeeegfgggiighiiiiiiiiiiiiiiiiiiiiiiiiihiihiiiiiiiiiiieghiiiiiigggggeeeeeccccccccccccc`acc`bacccc @DHCDZDN1:106:5:2203:1267:1116#0/1 GTAGCTGCCCGAGTAAAGCCAGTCCTGTGCTCCATTGTAGGGGTTAGGACCTTGATGGAACCACCTCGTCTTCCAGTCCTCCTCCTTTGTCCCTTTGGGG + bbbeeeeegggegbedfhhhhhghiiaeffghidgiihibfhiffg]e^egddgcegbfhigfggfee^cccdddbbcbbbccccccccbbbccccbb_a @DHCDZDN1:106:5:2203:1287:1122#0/1 GTGTGTGTGCCGTGGGGTGGGGTGTCACTATACTGTCCTAAGATACAAGCCAAGGGTAATCTCCGTGGACACACACGCTACCCTGCCTCCCATAATCCCT + _bbcceecegggcegfhbdcfggdcggfhagZegcggfhhhhghdggfgdee_baaZ^bcccccaacc^b`abcaacca_ccaYX``]b`aRSGS__bcb @DHCDZDN1:106:5:2203:1465:1126#0/1 GTCACGGACGGCGATACGGCGACCAGGGTACAGAACAGAGTCTGCCAGCCTTCTGGCCAGGAAGGAAATCTAGACTATCGTTCTACACATCCAGGCAGAA + _aaeeeeegggggiiiiiihF_aggfee^ccd_bddcccc`bccccccccbccccccccccccccaccbccccbccccbc`accdcbbcbbcbbca^^_b @DHCDZDN1:106:5:2203:1311:1161#0/1 GTGGAATGTGCGTCTTCAACGTTGTATTTTTTCTCACATACAAGCGGTGCAGCGACAATGGTAACTGCTACACATGACTTCCAGGGCCAACCATGACGCA + aaaeceeeggggghiiiiiiiiiigghiiiiihhiiiiiiiiiiiiighiiiiiiggeeeebdddddccccccccccbccccbcccacccccccccccca @DHCDZDN1:106:5:2203:1259:1184#0/1 CTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTAATGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTTCACCCCTCCTTA + _[_^cccc^eeJbRdZdfK`[^ebdP[WWHOOaZ^HHIIXXXNaIXbSZ_edBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB @DHCDZDN1:106:5:2203:1274:1191#0/1 GGGTACTGGAGACACGATGCTGTCTGAGCCAACAGAGGATTCGCTACTTTGAGTAAAAGGTGGTGAGCTGGATGTTTCTGACTGTACTGGCAGTTCGGCA + ___`cdeegggggighghfhgfadfhfffhbafZaafg_ghiihaegfgihae\_eghhhM\dY`Zaaccd]_b]]``bbZ`]bZ]``Y`aX^BBBBBBB @DHCDZDN1:106:5:2203:1416:1193#0/1 GGCCCAGGTCGGAAACGGAGCAGGTCAAAACTCCCGTGCTGATCAGTAGTGGGATCGCGCCTGTGAATAGCCACTGCACTCCAGCCTGGGCAACATAGCG + bbbeeeeegggggiiiiiiiiiii^ggiiihiiiiigiiiiiiiiihiifgiiiggggeccccbbcdddccccccbccccccccccbaccccccccbcca @DHCDZDN1:106:5:2203:1311:1197#0/1 CCTCGTGTGGCCTTTCATACAAGTCCTTATTTAGAGAACAAATGATTATGCTACCTTTGCACGGTCAGAATACCGCGGCCGTTTAACTGATGTCACCGGG + abbeeceeaggggiiiiiiiiiighhiiiiiifihihhghiiiihiiiiiiiiiiiiiiiiiihggfgihh`gggcdccccccccccccccccccccacc @DHCDZDN1:106:5:2203:1282:1244#0/1 CATCGAGGTCGTAAACCCTATTGTCGATATGGACTCTTAAACAGGATTGCGCTGTTATCCCTAGGGTAACTTGTTCCGTTGATCAAAGAAGTTTTGGATC + ___eecee_ceegfhhhhhfhhhgfhfdfgfhhffhhhfdddfhhhhh_eghhfdhffgggddceeZ^bddcddcbbc]`aaccdc`bbab_bcccc]`b @DHCDZDN1:106:5:2203:1437:1249#0/1 ATTATATTAGGAGTTAATTGGATATTTTTGGTATCAGGTTAGGTGAGAAGATGGGACTAGAATACGTCAATTTGGAAGTTGTCATCATATCAAGAGCTTT + ^aaeeeeegggceeggigiiiiihiiiiiiieeghhhifghiiggfhhhhghhiigiiiiiiiiihghifgiiigfgggeeeeeeedddddddccccccc @DHCDZDN1:106:5:2203:1526:1031#0/1 CATGTCTTTGGATAGAGAAATCAGCGTTTTCAGCTAGATTGCAAAACTGGTTTAAAGTATTCCCTCGGCGTGGGGCGAATACCAAGATCGGAAGAGCGGT + b_beeeeegfggcghhhfhihiiifgbfgiihiiiiiihiiiihiiiihifhhhhiieghhiiihiiiigcecccaaacccccccccccccaccacbac] @DHCDZDN1:106:5:2203:1732:1032#0/1 CCGCCACTCCGGATTCGGGGATCTGAACCCGACTCCCTTTCGATCGGCCGAGGGCAACGGAGGCCATCGCCCGTCCCTTCGGAACGGCGCTCGCCCATCC + ___c^cccg^egedfeghhha^c[aa^c_egad`defheRb_bHUS\^dbaZ\_aaaa_aaaaa_abGGWTZ_EWTT]bb_]OQT__BBBBBBBBBBBBB @DHCDZDN1:106:5:2203:1669:1033#0/1 GTGTGTGGTATGTGTGACAGTATAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGGAGGGGGTGTGTGTGTGTGTGGTGTGTGTATGTGTGG + aaaccceecgggghghghghgggghegdgdeefbfdfgffgefgfcfegegefefefgH\bH\bHGT`[`ZQZ^`^^``GQ[GQ[bG[_a^`]aGS]Y`B @DHCDZDN1:106:5:2203:1556:1034#0/1 AGAAGGGTTCAAAGACCAAACCAAGAAGATCGGATTGCCGAGACTATCACATCTTTGTAAACATGCAGTGTGAAGTAGGAGAAAGAAAGTGACAGGTAAC + J\^^cccceee^edZ^^^Yba`_c`cbcI^dfdbZ_ce]_c`U[\_SV__`bcdbd]V_dV\\`daZ]^aZ]]`_a_``R]TGZ_aa^YKYZ`]]^BBBB @DHCDZDN1:106:5:2203:1578:1048#0/1 GTTTTTTTTTTTTTTCCAGAGCTCAGCAGCATGTGTGTTCAAAGGGCTGTGAATGTTGGGTTCTCCTAGCAGGCTCTGGATGGACAGCAGGATGGGCCTG + ___cccccggggghffgd`V\c_c]]]X]dZ^ZMVMMU_bddbbba^_^KY]]_YTZ___QWWR]_]]__R_a_WJRY`RY]_XY][[[_aOSY_BBBBB @DHCDZDN1:106:5:2203:1725:1059#0/1 CCCGTGCGGAGGAGCGAGGAGGAAGGAAGCGCTTCCTCAAGATGCCTTTTTCTCCCATCAGCTGAGAAACAGTTGTAATAATGCAGAAATCTGCTGTGCC + bbbeeeeeggfggigigiiiiiiiiiiihhiiiiiiiggggggeeeeeeddddddcccccccccccccccccbccccdddcdccccb]b_bbccccbccc @DHCDZDN1:106:5:2203:1683:1061#0/1 TTTTCTTGGACTTTGGGGTCTTTTCTCAATTACCCAGTTGTATCCTGGCACCAATCCCTCTTTCAAAGCTGGGTAGAGACATGGTTTCTTTGCATGACTT + bbbeeeeegggggiiiiibfhiiiiiiiiiiiiiiiihiiihiiiiiiiiiiiiiiiiiiiiiiiiehhiiggggcceedddddbdccccccccdccccc --=-P56L6PDj2qGMqH8Kq7fJ-- From manuel.holtgrewe@fu-berlin.de Fri Jan 06 15:07:25 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RjAS4-0007gs-2q>; Fri, 06 Jan 2012 15:07:24 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1RjAS4-0005km-0T>; Fri, 06 Jan 2012 15:07:24 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RjAS3-0005St-Ue>; Fri, 06 Jan 2012 15:07:23 +0100 Message-ID: <4F06FFE1.6000809@fu-berlin.de> Date: Fri, 06 Jan 2012 15:06:25 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: SeqAn Development References: <1324484150.19199.29.camel@IR0912.bgbm.fu-berlin.de> <4EF217E3.1000605@fu-berlin.de> <1325856936.20283.5.camel@IR0912.bgbm.fu-berlin.de> In-Reply-To: <1325856936.20283.5.camel@IR0912.bgbm.fu-berlin.de> Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1325858844-000067B8-CD962AD9/3496853096-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=ALL_TRUSTED,FU_XPURGATE_SUSP Subject: Re: [Seqan-dev] CheckStreamFormat for FastQ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 06 Jan 2012 14:07:25 -0000 I tested the program on the file that you attached and it worked. Does the program detect the format of the small file, too? $ make file_detect [...] $ ./sandbox/holtgrew/demos/file_detect /tmp/lane_5_p1.fastq Detected FASTQ. Could you try again with a fresh checkout? On 01/06/2012 02:35 PM, Felix Heeger wrote: > Hi Manual, > > thank you for your effort. I checked your suggestion today and it did > not fix my problem. Also your example program can not identify my FASTQ > file. I am pretty sure it is valid FASTQ as other programs work fine on > it. I attached the first part of the file, if you want to have a look at > it. > > felix > > On Wed, 2011-12-21 at 18:31 +0100, Manuel Holtgrewe wrote: >> Felix, >> >> The documentation of checkStreamFormat() was misleading. I fixed it in >> [10948]. >> >> http://docs.seqan.de/seqan/dev2/?i=Function.checkStreamFormat >> >> (The documentation is regenerated every hour, so you might wait for a >> bit to see it). >> >> The following is a simple example program I compiled and tested. Please >> write another email, if the problem persists. >> >> HTH, >> Manuel >> >> #include >> #include >> >> #include >> #include >> >> int main(int argc, char ** argv) >> { >> using namespace seqan; >> >> if (argc != 2) >> return 1; >> std::fstream in(argv[1]); >> >> RecordReader > reader(in); >> AutoSeqStreamFormat tagSelector; >> bool b = checkStreamFormat(reader, tagSelector); >> if (!b) >> { >> std::cerr<< "Could not detect file format!"<< std::endl; >> return 1; >> } >> >> // b is true if any format was detected successfully. >> if (tagSelector.tagId == 1) >> std::cerr<< "Detected FASTA."<< std::endl; >> else if (tagSelector.tagId == 2) >> std::cerr<< "Detected FASTQ."<< std::endl; >> else >> std::cerr<< "Unknown file format!"<< std::endl; >> return 0; >> } >> >> >> On 12/21/2011 05:15 PM, Felix Heeger wrote: >>> Hi, >>> >>> I have to different functions I want to call depending on the fact if a >>> input file is fasta or fastq format. >>> >>> My approach to this is: >>> >>>> RecordReader > reader(inFile); >>>> if (checkStreamFormat(reader, Fasta())) >>>> { >>>> std::cerr<< "Input file format is fasta."<< std::endl; >>>> [call function for fasta] >>>> } >>>> else if (checkStreamFormat(reader, Fastq())) >>>> { >>>> std::cerr<< "Input file format is fastq."<< std::endl; >>>> [call function for fastq] >>>> } >>>> else >>>> { >>>> std::cerr<< "ERORR: Input file format is not fasta or fastq."<< std::endl; >>>> return -1; >>>> } >>> >>> This works fine for fasta. However my fastq file is not recognized. >>> I looked into the code for checkStreamFormat a bit and the file is not >>> recognized because the iterator in the readRecord function reaches >>> atEnd before the quality meta data for the 35th record is finished (l. 392). >>> This happens with two different fastq files. >>> >>> So my theory is the following: >>> In the checkStreamFormat function LimitRecordReaderInScope >>> is used. The documentation states that this prevents the stream from >>> "rebuffering". This probably prevents the reader from finishing to read >>> the complete record and the recognition of the file fails. >>> >>> I hope I could make myself clear. I can also provide my code and a sample >>> fastq file if it would be helpful. >>> >>> Cheers, >>> felix >>> >>> >>> >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > From fheeger@mi.fu-berlin.de Fri Jan 06 15:53:33 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RjBAh-0000g8-Qs>; Fri, 06 Jan 2012 15:53:31 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RjBAh-0006rL-Oh>; Fri, 06 Jan 2012 15:53:31 +0100 Received: from bgbm6.bgbm.fu-berlin.de ([160.45.63.17] helo=[192.168.1.143]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1RjBAh-0008OW-MU>; Fri, 06 Jan 2012 15:53:31 +0100 From: Felix Heeger To: SeqAn Development In-Reply-To: <4F06FFE1.6000809@fu-berlin.de> References: <1324484150.19199.29.camel@IR0912.bgbm.fu-berlin.de> <4EF217E3.1000605@fu-berlin.de> <1325856936.20283.5.camel@IR0912.bgbm.fu-berlin.de> <4F06FFE1.6000809@fu-berlin.de> Content-Type: text/plain; charset="UTF-8" Date: Fri, 06 Jan 2012 15:53:31 +0100 Message-ID: <1325861611.20283.11.camel@IR0912.bgbm.fu-berlin.de> Mime-Version: 1.0 X-Mailer: Evolution 2.32.2 Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.63.17 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1325861611-000067B8-3A8246D2/3496853096-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=ALL_TRUSTED,FU_XPURGATE_SUSP Subject: Re: [Seqan-dev] CheckStreamFormat for FastQ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 06 Jan 2012 14:53:34 -0000 Hi Manuel, I did a fresh check out, but the still the same problem. However if I remove the last 6 records from the file it will be recognized. I also removed the first 6 records to make sure it is the file size that is causing the issue and not a specific record. Same result. In short: it is working for me if the file size is <= 8KB. felix On Fri, 2012-01-06 at 15:06 +0100, Manuel Holtgrewe wrote: > I tested the program on the file that you attached and it worked. Does > the program detect the format of the small file, too? > > $ make file_detect > [...] > $ ./sandbox/holtgrew/demos/file_detect /tmp/lane_5_p1.fastq > Detected FASTQ. > > Could you try again with a fresh checkout? > > On 01/06/2012 02:35 PM, Felix Heeger wrote: > > Hi Manual, > > > > thank you for your effort. I checked your suggestion today and it did > > not fix my problem. Also your example program can not identify my FASTQ > > file. I am pretty sure it is valid FASTQ as other programs work fine on > > it. I attached the first part of the file, if you want to have a look at > > it. > > > > felix > > > > On Wed, 2011-12-21 at 18:31 +0100, Manuel Holtgrewe wrote: > >> Felix, > >> > >> The documentation of checkStreamFormat() was misleading. I fixed it in > >> [10948]. > >> > >> http://docs.seqan.de/seqan/dev2/?i=Function.checkStreamFormat > >> > >> (The documentation is regenerated every hour, so you might wait for a > >> bit to see it). > >> > >> The following is a simple example program I compiled and tested. Please > >> write another email, if the problem persists. > >> > >> HTH, > >> Manuel > >> > >> #include > >> #include > >> > >> #include > >> #include > >> > >> int main(int argc, char ** argv) > >> { > >> using namespace seqan; > >> > >> if (argc != 2) > >> return 1; > >> std::fstream in(argv[1]); > >> > >> RecordReader > reader(in); > >> AutoSeqStreamFormat tagSelector; > >> bool b = checkStreamFormat(reader, tagSelector); > >> if (!b) > >> { > >> std::cerr<< "Could not detect file format!"<< std::endl; > >> return 1; > >> } > >> > >> // b is true if any format was detected successfully. > >> if (tagSelector.tagId == 1) > >> std::cerr<< "Detected FASTA."<< std::endl; > >> else if (tagSelector.tagId == 2) > >> std::cerr<< "Detected FASTQ."<< std::endl; > >> else > >> std::cerr<< "Unknown file format!"<< std::endl; > >> return 0; > >> } > >> > >> > >> On 12/21/2011 05:15 PM, Felix Heeger wrote: > >>> Hi, > >>> > >>> I have to different functions I want to call depending on the fact if a > >>> input file is fasta or fastq format. > >>> > >>> My approach to this is: > >>> > >>>> RecordReader > reader(inFile); > >>>> if (checkStreamFormat(reader, Fasta())) > >>>> { > >>>> std::cerr<< "Input file format is fasta."<< std::endl; > >>>> [call function for fasta] > >>>> } > >>>> else if (checkStreamFormat(reader, Fastq())) > >>>> { > >>>> std::cerr<< "Input file format is fastq."<< std::endl; > >>>> [call function for fastq] > >>>> } > >>>> else > >>>> { > >>>> std::cerr<< "ERORR: Input file format is not fasta or fastq."<< std::endl; > >>>> return -1; > >>>> } > >>> > >>> This works fine for fasta. However my fastq file is not recognized. > >>> I looked into the code for checkStreamFormat a bit and the file is not > >>> recognized because the iterator in the readRecord function reaches > >>> atEnd before the quality meta data for the 35th record is finished (l. 392). > >>> This happens with two different fastq files. > >>> > >>> So my theory is the following: > >>> In the checkStreamFormat function LimitRecordReaderInScope > >>> is used. The documentation states that this prevents the stream from > >>> "rebuffering". This probably prevents the reader from finishing to read > >>> the complete record and the recognition of the file fails. > >>> > >>> I hope I could make myself clear. I can also provide my code and a sample > >>> fastq file if it would be helpful. > >>> > >>> Cheers, > >>> felix > >>> > >>> > >>> > >>> _______________________________________________ > >>> seqan-dev mailing list > >>> seqan-dev@lists.fu-berlin.de > >>> https://lists.fu-berlin.de/listinfo/seqan-dev > >> > >> _______________________________________________ > >> seqan-dev mailing list > >> seqan-dev@lists.fu-berlin.de > >> https://lists.fu-berlin.de/listinfo/seqan-dev > > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From manuel.holtgrewe@fu-berlin.de Fri Jan 06 16:53:16 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RjC6U-0002bO-Bb>; Fri, 06 Jan 2012 16:53:14 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RjC6U-0000Qv-8B>; Fri, 06 Jan 2012 16:53:14 +0100 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.100]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1RjC6U-0003bE-1T>; Fri, 06 Jan 2012 16:53:14 +0100 Message-ID: <4F0718E9.5010105@fu-berlin.de> Date: Fri, 06 Jan 2012 16:53:13 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: SeqAn Development References: <1324484150.19199.29.camel@IR0912.bgbm.fu-berlin.de> <4EF217E3.1000605@fu-berlin.de> <1325856936.20283.5.camel@IR0912.bgbm.fu-berlin.de> <4F06FFE1.6000809@fu-berlin.de> <1325861611.20283.11.camel@IR0912.bgbm.fu-berlin.de> In-Reply-To: <1325861611.20283.11.camel@IR0912.bgbm.fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1325865194-000067B8-0031D273/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] CheckStreamFormat for FastQ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 06 Jan 2012 15:53:16 -0000 What is your configuration (OS, 32/64 bit, compiler, version) On 01/06/2012 03:53 PM, Felix Heeger wrote: > Hi Manuel, > > I did a fresh check out, but the still the same problem. > > However if I remove the last 6 records from the file it will be > recognized. I also removed the first 6 records to make sure it is the > file size that is causing the issue and not a specific record. Same > result. > > In short: it is working for me if the file size is<= 8KB. > > felix > > On Fri, 2012-01-06 at 15:06 +0100, Manuel Holtgrewe wrote: >> I tested the program on the file that you attached and it worked. Does >> the program detect the format of the small file, too? >> >> $ make file_detect >> [...] >> $ ./sandbox/holtgrew/demos/file_detect /tmp/lane_5_p1.fastq >> Detected FASTQ. >> >> Could you try again with a fresh checkout? >> >> On 01/06/2012 02:35 PM, Felix Heeger wrote: >>> Hi Manual, >>> >>> thank you for your effort. I checked your suggestion today and it did >>> not fix my problem. Also your example program can not identify my FASTQ >>> file. I am pretty sure it is valid FASTQ as other programs work fine on >>> it. I attached the first part of the file, if you want to have a look at >>> it. >>> >>> felix >>> >>> On Wed, 2011-12-21 at 18:31 +0100, Manuel Holtgrewe wrote: >>>> Felix, >>>> >>>> The documentation of checkStreamFormat() was misleading. I fixed it in >>>> [10948]. >>>> >>>> http://docs.seqan.de/seqan/dev2/?i=Function.checkStreamFormat >>>> >>>> (The documentation is regenerated every hour, so you might wait for a >>>> bit to see it). >>>> >>>> The following is a simple example program I compiled and tested. Please >>>> write another email, if the problem persists. >>>> >>>> HTH, >>>> Manuel >>>> >>>> #include >>>> #include >>>> >>>> #include >>>> #include >>>> >>>> int main(int argc, char ** argv) >>>> { >>>> using namespace seqan; >>>> >>>> if (argc != 2) >>>> return 1; >>>> std::fstream in(argv[1]); >>>> >>>> RecordReader > reader(in); >>>> AutoSeqStreamFormat tagSelector; >>>> bool b = checkStreamFormat(reader, tagSelector); >>>> if (!b) >>>> { >>>> std::cerr<< "Could not detect file format!"<< std::endl; >>>> return 1; >>>> } >>>> >>>> // b is true if any format was detected successfully. >>>> if (tagSelector.tagId == 1) >>>> std::cerr<< "Detected FASTA."<< std::endl; >>>> else if (tagSelector.tagId == 2) >>>> std::cerr<< "Detected FASTQ."<< std::endl; >>>> else >>>> std::cerr<< "Unknown file format!"<< std::endl; >>>> return 0; >>>> } >>>> >>>> >>>> On 12/21/2011 05:15 PM, Felix Heeger wrote: >>>>> Hi, >>>>> >>>>> I have to different functions I want to call depending on the fact if a >>>>> input file is fasta or fastq format. >>>>> >>>>> My approach to this is: >>>>> >>>>>> RecordReader > reader(inFile); >>>>>> if (checkStreamFormat(reader, Fasta())) >>>>>> { >>>>>> std::cerr<< "Input file format is fasta."<< std::endl; >>>>>> [call function for fasta] >>>>>> } >>>>>> else if (checkStreamFormat(reader, Fastq())) >>>>>> { >>>>>> std::cerr<< "Input file format is fastq."<< std::endl; >>>>>> [call function for fastq] >>>>>> } >>>>>> else >>>>>> { >>>>>> std::cerr<< "ERORR: Input file format is not fasta or fastq."<< std::endl; >>>>>> return -1; >>>>>> } >>>>> >>>>> This works fine for fasta. However my fastq file is not recognized. >>>>> I looked into the code for checkStreamFormat a bit and the file is not >>>>> recognized because the iterator in the readRecord function reaches >>>>> atEnd before the quality meta data for the 35th record is finished (l. 392). >>>>> This happens with two different fastq files. >>>>> >>>>> So my theory is the following: >>>>> In the checkStreamFormat function LimitRecordReaderInScope >>>>> is used. The documentation states that this prevents the stream from >>>>> "rebuffering". This probably prevents the reader from finishing to read >>>>> the complete record and the recognition of the file fails. >>>>> >>>>> I hope I could make myself clear. I can also provide my code and a sample >>>>> fastq file if it would be helpful. >>>>> >>>>> Cheers, >>>>> felix >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> seqan-dev mailing list >>>>> seqan-dev@lists.fu-berlin.de >>>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>> >>>> _______________________________________________ >>>> seqan-dev mailing list >>>> seqan-dev@lists.fu-berlin.de >>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>> >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From fheeger@mi.fu-berlin.de Mon Jan 09 10:35:09 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RkBdD-0001mM-M7>; Mon, 09 Jan 2012 10:35:07 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RkBdD-00041A-Ir>; Mon, 09 Jan 2012 10:35:07 +0100 Received: from bgbm6.bgbm.fu-berlin.de ([160.45.63.17] helo=[192.168.1.143]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1RkBdD-0001ew-GZ>; Mon, 09 Jan 2012 10:35:07 +0100 From: Felix Heeger To: SeqAn Development In-Reply-To: <4F0718E9.5010105@fu-berlin.de> References: <1324484150.19199.29.camel@IR0912.bgbm.fu-berlin.de> <4EF217E3.1000605@fu-berlin.de> <1325856936.20283.5.camel@IR0912.bgbm.fu-berlin.de> <4F06FFE1.6000809@fu-berlin.de> <1325861611.20283.11.camel@IR0912.bgbm.fu-berlin.de> <4F0718E9.5010105@fu-berlin.de> Content-Type: text/plain; charset="UTF-8" Date: Mon, 09 Jan 2012 10:35:09 +0100 Message-ID: <1326101709.1539.4.camel@IR0912.bgbm.fu-berlin.de> Mime-Version: 1.0 X-Mailer: Evolution 2.32.2 Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.63.17 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326101707-000067B8-ED38E990/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] CheckStreamFormat for FastQ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 09 Jan 2012 09:35:09 -0000 Hi, My configuration: Ubuntu 11.04 64bit 64 bit processor gcc version 4.5.2 felix On Fri, 2012-01-06 at 16:53 +0100, Manuel Holtgrewe wrote: > What is your configuration (OS, 32/64 bit, compiler, version) > > On 01/06/2012 03:53 PM, Felix Heeger wrote: > > Hi Manuel, > > > > I did a fresh check out, but the still the same problem. > > > > However if I remove the last 6 records from the file it will be > > recognized. I also removed the first 6 records to make sure it is the > > file size that is causing the issue and not a specific record. Same > > result. > > > > In short: it is working for me if the file size is<= 8KB. > > > > felix > > > > On Fri, 2012-01-06 at 15:06 +0100, Manuel Holtgrewe wrote: > >> I tested the program on the file that you attached and it worked. Does > >> the program detect the format of the small file, too? > >> > >> $ make file_detect > >> [...] > >> $ ./sandbox/holtgrew/demos/file_detect /tmp/lane_5_p1.fastq > >> Detected FASTQ. > >> > >> Could you try again with a fresh checkout? > >> > >> On 01/06/2012 02:35 PM, Felix Heeger wrote: > >>> Hi Manual, > >>> > >>> thank you for your effort. I checked your suggestion today and it did > >>> not fix my problem. Also your example program can not identify my FASTQ > >>> file. I am pretty sure it is valid FASTQ as other programs work fine on > >>> it. I attached the first part of the file, if you want to have a look at > >>> it. > >>> > >>> felix > >>> > >>> On Wed, 2011-12-21 at 18:31 +0100, Manuel Holtgrewe wrote: > >>>> Felix, > >>>> > >>>> The documentation of checkStreamFormat() was misleading. I fixed it in > >>>> [10948]. > >>>> > >>>> http://docs.seqan.de/seqan/dev2/?i=Function.checkStreamFormat > >>>> > >>>> (The documentation is regenerated every hour, so you might wait for a > >>>> bit to see it). > >>>> > >>>> The following is a simple example program I compiled and tested. Please > >>>> write another email, if the problem persists. > >>>> > >>>> HTH, > >>>> Manuel > >>>> > >>>> #include > >>>> #include > >>>> > >>>> #include > >>>> #include > >>>> > >>>> int main(int argc, char ** argv) > >>>> { > >>>> using namespace seqan; > >>>> > >>>> if (argc != 2) > >>>> return 1; > >>>> std::fstream in(argv[1]); > >>>> > >>>> RecordReader > reader(in); > >>>> AutoSeqStreamFormat tagSelector; > >>>> bool b = checkStreamFormat(reader, tagSelector); > >>>> if (!b) > >>>> { > >>>> std::cerr<< "Could not detect file format!"<< std::endl; > >>>> return 1; > >>>> } > >>>> > >>>> // b is true if any format was detected successfully. > >>>> if (tagSelector.tagId == 1) > >>>> std::cerr<< "Detected FASTA."<< std::endl; > >>>> else if (tagSelector.tagId == 2) > >>>> std::cerr<< "Detected FASTQ."<< std::endl; > >>>> else > >>>> std::cerr<< "Unknown file format!"<< std::endl; > >>>> return 0; > >>>> } > >>>> > >>>> > >>>> On 12/21/2011 05:15 PM, Felix Heeger wrote: > >>>>> Hi, > >>>>> > >>>>> I have to different functions I want to call depending on the fact if a > >>>>> input file is fasta or fastq format. > >>>>> > >>>>> My approach to this is: > >>>>> > >>>>>> RecordReader > reader(inFile); > >>>>>> if (checkStreamFormat(reader, Fasta())) > >>>>>> { > >>>>>> std::cerr<< "Input file format is fasta."<< std::endl; > >>>>>> [call function for fasta] > >>>>>> } > >>>>>> else if (checkStreamFormat(reader, Fastq())) > >>>>>> { > >>>>>> std::cerr<< "Input file format is fastq."<< std::endl; > >>>>>> [call function for fastq] > >>>>>> } > >>>>>> else > >>>>>> { > >>>>>> std::cerr<< "ERORR: Input file format is not fasta or fastq."<< std::endl; > >>>>>> return -1; > >>>>>> } > >>>>> > >>>>> This works fine for fasta. However my fastq file is not recognized. > >>>>> I looked into the code for checkStreamFormat a bit and the file is not > >>>>> recognized because the iterator in the readRecord function reaches > >>>>> atEnd before the quality meta data for the 35th record is finished (l. 392). > >>>>> This happens with two different fastq files. > >>>>> > >>>>> So my theory is the following: > >>>>> In the checkStreamFormat function LimitRecordReaderInScope > >>>>> is used. The documentation states that this prevents the stream from > >>>>> "rebuffering". This probably prevents the reader from finishing to read > >>>>> the complete record and the recognition of the file fails. > >>>>> > >>>>> I hope I could make myself clear. I can also provide my code and a sample > >>>>> fastq file if it would be helpful. > >>>>> > >>>>> Cheers, > >>>>> felix > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> seqan-dev mailing list > >>>>> seqan-dev@lists.fu-berlin.de > >>>>> https://lists.fu-berlin.de/listinfo/seqan-dev > >>>> > >>>> _______________________________________________ > >>>> seqan-dev mailing list > >>>> seqan-dev@lists.fu-berlin.de > >>>> https://lists.fu-berlin.de/listinfo/seqan-dev > >>> > >> > >> _______________________________________________ > >> seqan-dev mailing list > >> seqan-dev@lists.fu-berlin.de > >> https://lists.fu-berlin.de/listinfo/seqan-dev > > > > > > > > _______________________________________________ > > seqan-dev mailing list > > seqan-dev@lists.fu-berlin.de > > https://lists.fu-berlin.de/listinfo/seqan-dev > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From manuel.holtgrewe@fu-berlin.de Mon Jan 09 11:10:33 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RkCBT-0002xc-9x>; Mon, 09 Jan 2012 11:10:31 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1RkCBT-0004dB-7r>; Mon, 09 Jan 2012 11:10:31 +0100 Received: from ecoli.imp.fu-berlin.de ([160.45.111.133]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RkCBT-0004Um-5i>; Mon, 09 Jan 2012 11:10:31 +0100 Message-ID: <4F0ABCDA.3060408@fu-berlin.de> Date: Mon, 09 Jan 2012 11:09:30 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: SeqAn Development References: <1324484150.19199.29.camel@IR0912.bgbm.fu-berlin.de> <4EF217E3.1000605@fu-berlin.de> <1325856936.20283.5.camel@IR0912.bgbm.fu-berlin.de> <4F06FFE1.6000809@fu-berlin.de> <1325861611.20283.11.camel@IR0912.bgbm.fu-berlin.de> <4F0718E9.5010105@fu-berlin.de> <1326101709.1539.4.camel@IR0912.bgbm.fu-berlin.de> In-Reply-To: <1326101709.1539.4.camel@IR0912.bgbm.fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.111.133 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1326103831-000067B8-2DA3C123/3498247028-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000020, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=ALL_TRUSTED,FU_XPURGATE_SUSP Subject: Re: [Seqan-dev] CheckStreamFormat for FastQ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 09 Jan 2012 10:10:33 -0000 OK, apparently the file was converted from unix line endings to windows line endings through the list. r1018 has a fix to the bug. Try updating and report back if the problem is not fixed yet. HTH On 01/09/2012 10:35 AM, Felix Heeger wrote: > Hi, > > My configuration: > Ubuntu 11.04 64bit > 64 bit processor > gcc version 4.5.2 > > felix > > On Fri, 2012-01-06 at 16:53 +0100, Manuel Holtgrewe wrote: >> What is your configuration (OS, 32/64 bit, compiler, version) >> >> On 01/06/2012 03:53 PM, Felix Heeger wrote: >>> Hi Manuel, >>> >>> I did a fresh check out, but the still the same problem. >>> >>> However if I remove the last 6 records from the file it will be >>> recognized. I also removed the first 6 records to make sure it is the >>> file size that is causing the issue and not a specific record. Same >>> result. >>> >>> In short: it is working for me if the file size is<= 8KB. >>> >>> felix >>> >>> On Fri, 2012-01-06 at 15:06 +0100, Manuel Holtgrewe wrote: >>>> I tested the program on the file that you attached and it worked. Does >>>> the program detect the format of the small file, too? >>>> >>>> $ make file_detect >>>> [...] >>>> $ ./sandbox/holtgrew/demos/file_detect /tmp/lane_5_p1.fastq >>>> Detected FASTQ. >>>> >>>> Could you try again with a fresh checkout? >>>> >>>> On 01/06/2012 02:35 PM, Felix Heeger wrote: >>>>> Hi Manual, >>>>> >>>>> thank you for your effort. I checked your suggestion today and it did >>>>> not fix my problem. Also your example program can not identify my FASTQ >>>>> file. I am pretty sure it is valid FASTQ as other programs work fine on >>>>> it. I attached the first part of the file, if you want to have a look at >>>>> it. >>>>> >>>>> felix >>>>> >>>>> On Wed, 2011-12-21 at 18:31 +0100, Manuel Holtgrewe wrote: >>>>>> Felix, >>>>>> >>>>>> The documentation of checkStreamFormat() was misleading. I fixed it in >>>>>> [10948]. >>>>>> >>>>>> http://docs.seqan.de/seqan/dev2/?i=Function.checkStreamFormat >>>>>> >>>>>> (The documentation is regenerated every hour, so you might wait for a >>>>>> bit to see it). >>>>>> >>>>>> The following is a simple example program I compiled and tested. Please >>>>>> write another email, if the problem persists. >>>>>> >>>>>> HTH, >>>>>> Manuel >>>>>> >>>>>> #include >>>>>> #include >>>>>> >>>>>> #include >>>>>> #include >>>>>> >>>>>> int main(int argc, char ** argv) >>>>>> { >>>>>> using namespace seqan; >>>>>> >>>>>> if (argc != 2) >>>>>> return 1; >>>>>> std::fstream in(argv[1]); >>>>>> >>>>>> RecordReader > reader(in); >>>>>> AutoSeqStreamFormat tagSelector; >>>>>> bool b = checkStreamFormat(reader, tagSelector); >>>>>> if (!b) >>>>>> { >>>>>> std::cerr<< "Could not detect file format!"<< std::endl; >>>>>> return 1; >>>>>> } >>>>>> >>>>>> // b is true if any format was detected successfully. >>>>>> if (tagSelector.tagId == 1) >>>>>> std::cerr<< "Detected FASTA."<< std::endl; >>>>>> else if (tagSelector.tagId == 2) >>>>>> std::cerr<< "Detected FASTQ."<< std::endl; >>>>>> else >>>>>> std::cerr<< "Unknown file format!"<< std::endl; >>>>>> return 0; >>>>>> } >>>>>> >>>>>> >>>>>> On 12/21/2011 05:15 PM, Felix Heeger wrote: >>>>>>> Hi, >>>>>>> >>>>>>> I have to different functions I want to call depending on the fact if a >>>>>>> input file is fasta or fastq format. >>>>>>> >>>>>>> My approach to this is: >>>>>>> >>>>>>>> RecordReader > reader(inFile); >>>>>>>> if (checkStreamFormat(reader, Fasta())) >>>>>>>> { >>>>>>>> std::cerr<< "Input file format is fasta."<< std::endl; >>>>>>>> [call function for fasta] >>>>>>>> } >>>>>>>> else if (checkStreamFormat(reader, Fastq())) >>>>>>>> { >>>>>>>> std::cerr<< "Input file format is fastq."<< std::endl; >>>>>>>> [call function for fastq] >>>>>>>> } >>>>>>>> else >>>>>>>> { >>>>>>>> std::cerr<< "ERORR: Input file format is not fasta or fastq."<< std::endl; >>>>>>>> return -1; >>>>>>>> } >>>>>>> >>>>>>> This works fine for fasta. However my fastq file is not recognized. >>>>>>> I looked into the code for checkStreamFormat a bit and the file is not >>>>>>> recognized because the iterator in the readRecord function reaches >>>>>>> atEnd before the quality meta data for the 35th record is finished (l. 392). >>>>>>> This happens with two different fastq files. >>>>>>> >>>>>>> So my theory is the following: >>>>>>> In the checkStreamFormat function LimitRecordReaderInScope >>>>>>> is used. The documentation states that this prevents the stream from >>>>>>> "rebuffering". This probably prevents the reader from finishing to read >>>>>>> the complete record and the recognition of the file fails. >>>>>>> >>>>>>> I hope I could make myself clear. I can also provide my code and a sample >>>>>>> fastq file if it would be helpful. >>>>>>> >>>>>>> Cheers, >>>>>>> felix >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> seqan-dev mailing list >>>>>>> seqan-dev@lists.fu-berlin.de >>>>>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>>>> >>>>>> _______________________________________________ >>>>>> seqan-dev mailing list >>>>>> seqan-dev@lists.fu-berlin.de >>>>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>>> >>>> >>>> _______________________________________________ >>>> seqan-dev mailing list >>>> seqan-dev@lists.fu-berlin.de >>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>> >>> >>> >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From fheeger@mi.fu-berlin.de Mon Jan 09 13:02:55 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RkDwC-000724-SZ>; Mon, 09 Jan 2012 13:02:53 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RkDwC-0000c2-Q3>; Mon, 09 Jan 2012 13:02:52 +0100 Received: from bgbm6.bgbm.fu-berlin.de ([160.45.63.17] helo=[192.168.1.143]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1RkDwC-0004h3-Nh>; Mon, 09 Jan 2012 13:02:52 +0100 From: Felix Heeger To: SeqAn Development In-Reply-To: <4F0ABCDA.3060408@fu-berlin.de> References: <1324484150.19199.29.camel@IR0912.bgbm.fu-berlin.de> <4EF217E3.1000605@fu-berlin.de> <1325856936.20283.5.camel@IR0912.bgbm.fu-berlin.de> <4F06FFE1.6000809@fu-berlin.de> <1325861611.20283.11.camel@IR0912.bgbm.fu-berlin.de> <4F0718E9.5010105@fu-berlin.de> <1326101709.1539.4.camel@IR0912.bgbm.fu-berlin.de> <4F0ABCDA.3060408@fu-berlin.de> Content-Type: text/plain; charset="UTF-8" Date: Mon, 09 Jan 2012 13:02:52 +0100 Message-ID: <1326110572.1539.6.camel@IR0912.bgbm.fu-berlin.de> Mime-Version: 1.0 X-Mailer: Evolution 2.32.2 Content-Transfer-Encoding: 7bit X-Originating-IP: 160.45.63.17 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326110572-000067B8-06CA4B44/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000005, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] CheckStreamFormat for FastQ X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 09 Jan 2012 12:02:55 -0000 Hi, its working fine now. Thank you very much for your help. felix On Mon, 2012-01-09 at 11:09 +0100, Manuel Holtgrewe wrote: > OK, apparently the file was converted from unix line endings to windows > line endings through the list. > > r1018 has a fix to the bug. Try updating and report back if the problem > is not fixed yet. > > HTH > > On 01/09/2012 10:35 AM, Felix Heeger wrote: > > Hi, > > > > My configuration: > > Ubuntu 11.04 64bit > > 64 bit processor > > gcc version 4.5.2 > > > > felix > > > > On Fri, 2012-01-06 at 16:53 +0100, Manuel Holtgrewe wrote: > >> What is your configuration (OS, 32/64 bit, compiler, version) > >> > >> On 01/06/2012 03:53 PM, Felix Heeger wrote: > >>> Hi Manuel, > >>> > >>> I did a fresh check out, but the still the same problem. > >>> > >>> However if I remove the last 6 records from the file it will be > >>> recognized. I also removed the first 6 records to make sure it is the > >>> file size that is causing the issue and not a specific record. Same > >>> result. > >>> > >>> In short: it is working for me if the file size is<= 8KB. > >>> > >>> felix > >>> > >>> On Fri, 2012-01-06 at 15:06 +0100, Manuel Holtgrewe wrote: > >>>> I tested the program on the file that you attached and it worked. Does > >>>> the program detect the format of the small file, too? > >>>> > >>>> $ make file_detect > >>>> [...] > >>>> $ ./sandbox/holtgrew/demos/file_detect /tmp/lane_5_p1.fastq > >>>> Detected FASTQ. > >>>> > >>>> Could you try again with a fresh checkout? > >>>> > >>>> On 01/06/2012 02:35 PM, Felix Heeger wrote: > >>>>> Hi Manual, > >>>>> > >>>>> thank you for your effort. I checked your suggestion today and it did > >>>>> not fix my problem. Also your example program can not identify my FASTQ > >>>>> file. I am pretty sure it is valid FASTQ as other programs work fine on > >>>>> it. I attached the first part of the file, if you want to have a look at > >>>>> it. > >>>>> > >>>>> felix > >>>>> > >>>>> On Wed, 2011-12-21 at 18:31 +0100, Manuel Holtgrewe wrote: > >>>>>> Felix, > >>>>>> > >>>>>> The documentation of checkStreamFormat() was misleading. I fixed it in > >>>>>> [10948]. > >>>>>> > >>>>>> http://docs.seqan.de/seqan/dev2/?i=Function.checkStreamFormat > >>>>>> > >>>>>> (The documentation is regenerated every hour, so you might wait for a > >>>>>> bit to see it). > >>>>>> > >>>>>> The following is a simple example program I compiled and tested. Please > >>>>>> write another email, if the problem persists. > >>>>>> > >>>>>> HTH, > >>>>>> Manuel > >>>>>> > >>>>>> #include > >>>>>> #include > >>>>>> > >>>>>> #include > >>>>>> #include > >>>>>> > >>>>>> int main(int argc, char ** argv) > >>>>>> { > >>>>>> using namespace seqan; > >>>>>> > >>>>>> if (argc != 2) > >>>>>> return 1; > >>>>>> std::fstream in(argv[1]); > >>>>>> > >>>>>> RecordReader > reader(in); > >>>>>> AutoSeqStreamFormat tagSelector; > >>>>>> bool b = checkStreamFormat(reader, tagSelector); > >>>>>> if (!b) > >>>>>> { > >>>>>> std::cerr<< "Could not detect file format!"<< std::endl; > >>>>>> return 1; > >>>>>> } > >>>>>> > >>>>>> // b is true if any format was detected successfully. > >>>>>> if (tagSelector.tagId == 1) > >>>>>> std::cerr<< "Detected FASTA."<< std::endl; > >>>>>> else if (tagSelector.tagId == 2) > >>>>>> std::cerr<< "Detected FASTQ."<< std::endl; > >>>>>> else > >>>>>> std::cerr<< "Unknown file format!"<< std::endl; > >>>>>> return 0; > >>>>>> } > >>>>>> > >>>>>> > >>>>>> On 12/21/2011 05:15 PM, Felix Heeger wrote: > >>>>>>> Hi, > >>>>>>> > >>>>>>> I have to different functions I want to call depending on the fact if a > >>>>>>> input file is fasta or fastq format. > >>>>>>> > >>>>>>> My approach to this is: > >>>>>>> > >>>>>>>> RecordReader > reader(inFile); > >>>>>>>> if (checkStreamFormat(reader, Fasta())) > >>>>>>>> { > >>>>>>>> std::cerr<< "Input file format is fasta."<< std::endl; > >>>>>>>> [call function for fasta] > >>>>>>>> } > >>>>>>>> else if (checkStreamFormat(reader, Fastq())) > >>>>>>>> { > >>>>>>>> std::cerr<< "Input file format is fastq."<< std::endl; > >>>>>>>> [call function for fastq] > >>>>>>>> } > >>>>>>>> else > >>>>>>>> { > >>>>>>>> std::cerr<< "ERORR: Input file format is not fasta or fastq."<< std::endl; > >>>>>>>> return -1; > >>>>>>>> } > >>>>>>> > >>>>>>> This works fine for fasta. However my fastq file is not recognized. > >>>>>>> I looked into the code for checkStreamFormat a bit and the file is not > >>>>>>> recognized because the iterator in the readRecord function reaches > >>>>>>> atEnd before the quality meta data for the 35th record is finished (l. 392). > >>>>>>> This happens with two different fastq files. > >>>>>>> > >>>>>>> So my theory is the following: > >>>>>>> In the checkStreamFormat function LimitRecordReaderInScope > >>>>>>> is used. The documentation states that this prevents the stream from > >>>>>>> "rebuffering". This probably prevents the reader from finishing to read > >>>>>>> the complete record and the recognition of the file fails. > >>>>>>> > >>>>>>> I hope I could make myself clear. I can also provide my code and a sample > >>>>>>> fastq file if it would be helpful. > >>>>>>> > >>>>>>> Cheers, > >>>>>>> felix > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> seqan-dev mailing list > >>>>>>> seqan-dev@lists.fu-berlin.de > >>>>>>> https://lists.fu-berlin.de/listinfo/seqan-dev > >>>>>> > >>>>>> _______________________________________________ > >>>>>> seqan-dev mailing list > >>>>>> seqan-dev@lists.fu-berlin.de > >>>>>> https://lists.fu-berlin.de/listinfo/seqan-dev > >>>>> > >>>> > >>>> _______________________________________________ > >>>> seqan-dev mailing list > >>>> seqan-dev@lists.fu-berlin.de > >>>> https://lists.fu-berlin.de/listinfo/seqan-dev > >>> > >>> > >>> > >>> _______________________________________________ > >>> seqan-dev mailing list > >>> seqan-dev@lists.fu-berlin.de > >>> https://lists.fu-berlin.de/listinfo/seqan-dev > >> > >> _______________________________________________ > >> seqan-dev mailing list > >> seqan-dev@lists.fu-berlin.de > >> https://lists.fu-berlin.de/listinfo/seqan-dev > > > > > > > > _______________________________________________ > > seqan-dev mailing list > > seqan-dev@lists.fu-berlin.de > > https://lists.fu-berlin.de/listinfo/seqan-dev > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From ZickmannF@rki.de Wed Jan 11 13:58:36 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RkxlD-0001tg-2v>; Wed, 11 Jan 2012 13:58:35 +0100 Received: from m3-bn.bund.de ([77.87.228.75]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RkxlC-0004NI-Vr>; Wed, 11 Jan 2012 13:58:35 +0100 Received: from m3.mfw.bn.ivbb.bund.de (localhost [127.0.0.1]) by m3-bn.bund.de (8.14.3/8.14.3) with ESMTP id q0BCwYwI002374 for ; Wed, 11 Jan 2012 13:58:34 +0100 (CET) Received: (from localhost) by m3.mfw.bn.ivbb.bund.de (MSCAN) id 4/m3.mfw.bn.ivbb.bund.de/smtp-gw/mscan; Wed Jan 11 13:58:34 2012 X-P350-Id: 786c3bba340aedde From: "Zickmann, Franziska" To: "seqan-dev@lists.fu-berlin.de" Date: Wed, 11 Jan 2012 13:58:29 +0100 Thread-Topic: Sandbox download in seqan tutorial Thread-Index: AczQYLdY/Ce55BtpSHqAgqZ4iDlTbw== Message-ID: <76C738ACAD4EDA429A07ED7161758159903B44849E@semail08.rki.local> Accept-Language: de-DE Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE x-tm-as-product-ver: SMEX-8.0.0.4177-6.500.1024-18638.005 x-tm-as-result: No--39.297500-0.000000-31 x-tm-as-user-approved-sender: Yes x-tm-as-user-blocked-sender: No Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 77.87.228.75 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326286715-000067B8-F1FBAC65/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.011787, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.5 required=5.0 tests=TO_ADDRESS_EQ_REAL Subject: [Seqan-dev] Sandbox download in seqan tutorial X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 11 Jan 2012 12:58:36 -0000 Hi, think I spotted a minor "left-over" from the moving of the seqan-site: =20 When I tried to download my_sandox.zip as explained in the "Getting Started= " tutorial (wget http://trac.mi.fu-berlin.de/seqan/attachment/wiki/Tutorial/GettingSta= rted/my_sandbox.zip), I get an error message telling me that it cannot be f= ound.=20 Can you please add the updated link? Thank you,=20 Cheers, Franzi= From okko73313@gmail.com Thu Jan 12 15:00:05 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RlLCG-0007el-0s>; Thu, 12 Jan 2012 15:00:04 +0100 Received: from mail-wi0-f182.google.com ([209.85.212.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RlLCF-0000rc-TN>; Thu, 12 Jan 2012 15:00:04 +0100 Received: by wibhm4 with SMTP id hm4so1858075wib.13 for ; Thu, 12 Jan 2012 06:00:03 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:reply-to:sender:date:x-google-sender-auth:message-id :subject:from:to:content-type; bh=6arm9fP+k20jkgeJ2dF/nPVlVK3v9vh27AL5HtaJmEI=; b=STa0FC9hDLU2tNf9QS4IXb1tQ0jy21Zkib6fL2SJlfNs66CBtWvWQOc+qkxzaU7RW6 6/1YI2krJ1MRmo5r+/FroumtRu+4nzkVez1S4nIb/fNep7LFw+/kt2R9XddSfqp3zNQe GhqJ5FXdBnqrVB7EPTsCxef4ml68LM/DocJHc= MIME-Version: 1.0 Received: by 10.180.106.202 with SMTP id gw10mr655855wib.3.1326376803623; Thu, 12 Jan 2012 06:00:03 -0800 (PST) Sender: okko73313@gmail.com Received: by 10.180.18.41 with HTTP; Thu, 12 Jan 2012 06:00:03 -0800 (PST) Date: Thu, 12 Jan 2012 15:00:03 +0100 X-Google-Sender-Auth: qhrZoutrsC1teteuaasVyh_Qew8 Message-ID: From: Konstantin Okonechnikov To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/mixed; boundary=e89a8f234bfb37e39204b6552aec X-Originating-IP: 209.85.212.182 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326376804-000067B8-0B8AA95C/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.209922, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] small patch for CommandLineParser X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: k.okonechnikov@gmail.com, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 12 Jan 2012 14:00:05 -0000 --e89a8f234bfb37e39204b6552aec Content-Type: text/plain; charset=ISO-8859-1 Hi! The patch file is attached. The patch feature: show an error message when the required number of command line parameters doesn't match the number of given parameters. Best regards, Konstantin --e89a8f234bfb37e39204b6552aec Content-Type: text/x-patch; charset=US-ASCII; name="patch.diff" Content-Disposition: attachment; filename="patch.diff" Content-Transfer-Encoding: base64 X-Attachment-Id: f_gxbudxkb0 SW5kZXg6IGNvcmUvaW5jbHVkZS9zZXFhbi9taXNjL21pc2NfY21kcGFyc2VyLmgKPT09PT09PT09 PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09PT09 PQotLS0gY29yZS9pbmNsdWRlL3NlcWFuL21pc2MvbWlzY19jbWRwYXJzZXIuaAkocmV2aXNpb24g MTEwNTEpCisrKyBjb3JlL2luY2x1ZGUvc2VxYW4vbWlzYy9taXNjX2NtZHBhcnNlci5oCSh3b3Jr aW5nIGNvcHkpCkBAIC0xNDI1LDEyICsxNDI1LDE5IEBACiAgICAgICAgIGhlbHAobWUsIGVzdHJl YW0pOwogICAgICAgICByZXR1cm4gZmFsc2U7CiAgICAgfQotCWlmIChhcmdjID09IDEgJiYgbWUu cmVxdWlyZWRfYXJndW1lbnRzID4gMCkKKwlpZiAoIGxlbmd0aChtZS5hcmd1bWVudHMpIDwgbWUu cmVxdWlyZWRfYXJndW1lbnRzICkKIAl7Ci0JCXNob3J0SGVscChtZSwgZXN0cmVhbSk7CS8vIHBy aW50IHNob3J0IGhlbHAgYW5kIGV4aXQKLQkJcmV0dXJuIDA7CisgICAgICAgIGlmIChhcmdjID09 IDEpIHsKKyAgICAgICAgICAgIHNob3J0SGVscChtZSwgZXN0cmVhbSk7CS8vIHByaW50IHNob3J0 IGhlbHAgYW5kIGV4aXQKKwkgICAgfSBlbHNlIHsgCisgICAgICAgICAgICBfc3RyZWFtV3JpdGUo ZXN0cmVhbSwgbWUuYXBwTmFtZSk7ICAgICAgCisgICAgICAgICAgICBfc3RyZWFtV3JpdGUoZXN0 cmVhbSwgIjogbnVtYmVyIG9mIHJlcXVpcmVkIGFyZ3VtZW50cyBpcyAiKTsKKyAgICAgICAgICAg IF9zdHJlYW1QdXRJbnQoZXN0cmVhbSwgbWUucmVxdWlyZWRfYXJndW1lbnRzKTsgIAorICAgICAg ICAgICAgX3N0cmVhbVdyaXRlKGVzdHJlYW0sICJcbiIpOworCQl9CisgICAgICAgIHJldHVybiBm YWxzZTsKIAl9Ci0JcmV0dXJuIF9hbGxNYW5kYXRvcnlTZXQobWUpICYmIChsZW5ndGgobWUuYXJn dW1lbnRzKSA+PSBtZS5yZXF1aXJlZF9hcmd1bWVudHMpOworCXJldHVybiBfYWxsTWFuZGF0b3J5 U2V0KG1lKTsKIH0KIAogaW5saW5lIGJvb2wK --e89a8f234bfb37e39204b6552aec-- From lidoslidos@gmail.com Thu Jan 12 16:31:38 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RlMcr-0002NJ-Ts>; Thu, 12 Jan 2012 16:31:38 +0100 Received: from mail-gx0-f182.google.com ([209.85.161.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RlMcr-0004Xu-NR>; Thu, 12 Jan 2012 16:31:37 +0100 Received: by ggki1 with SMTP id i1so1337842ggk.13 for ; Thu, 12 Jan 2012 07:31:36 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:from:date:message-id:subject:to:content-type; bh=K04YuId384k8UQyZHy5OL1EMeNDTXhBHHqvVhD9PuvY=; b=pNyoMVfQYuCnTQ53QqD76W5RAaU7MWCK3/ZZCKFeWaJjODZPkce+RUoeNTWDv/PpC3 uyBsq6TAjeRAtAqGMBQ8BhcvPzRNd3LcGO7Bvekpc44hsOXcuK/5qOGUFE6EMYEpn19T DIGRpEuVoJ3KzOzo7wxKRFKZURdf4HrUtmBhA= Received: by 10.50.183.199 with SMTP id eo7mr4661375igc.5.1326382296149; Thu, 12 Jan 2012 07:31:36 -0800 (PST) MIME-Version: 1.0 Received: by 10.42.164.8 with HTTP; Thu, 12 Jan 2012 07:30:55 -0800 (PST) From: Lidia Gorbunova Date: Thu, 12 Jan 2012 16:30:55 +0100 Message-ID: To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=14dae934042d99306304b6567170 X-Originating-IP: 209.85.161.182 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326382297-000067B8-D5C66D5F/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.438456, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.6 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_FONT_BIG,HTML_MESSAGE,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] OT X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 12 Jan 2012 15:31:38 -0000 --14dae934042d99306304b6567170 Content-Type: text/plain; charset=ISO-8859-1 *Kannst du noch den anderen vertrauen?* * * Wir suchen Teilnehmerinnen und Teilnehmer fuer eine soziologische Studie, in der wir das zwischenmenschliche Vertrauen untersuchen moechten. Jeder Teilnehmer erhaelt garantiert 2.50 Euro, und kann im Laufe des Experiments bis zu 10 Euro bekommen. Dafuer muss man nur an einem einfachen Vertrauenspiel teilnehmen. Psychologiestudierende erhalten Punkte (Credits). Dauer: circa 30 minuten. *Bei Interesse bitte* *E-Mail an:* *lidos@zedat.fu-berlin.de* * * *Also in English!* --14dae934042d99306304b6567170 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Kannst du noch den anderen vertrauen?

=A0

Wir suchen Teilnehmerinnen un= d Teilnehmer fuer eine soziologische Studie, in der wir das zwischenmenschl= iche Vertrauen untersuchen moechten.

Jeder Teilnehmer erhaelt gara= ntiert 2.50 Euro, und kann im Laufe des Experiments bis zu 10 Euro bekommen= .=A0Dafuer muss man = nur an einem einfachen Vertrauenspiel teilnehmen.

Psychologiestudierende erhalt= en Punkte (Credits).

=A0=A0=A0=A0=A0=A0=A0 Dauer:=A0=A0circa= =A030=A0minuten.

=A0

Bei Inte= resse bitte

E-Mail an:

lidos@zedat.fu-berlin.de


Also in English!

--14dae934042d99306304b6567170-- From neilniu.cn@gmail.com Fri Jan 13 01:10:30 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RlUiy-00019c-0x>; Fri, 13 Jan 2012 01:10:28 +0100 Received: from mail-qy0-f182.google.com ([209.85.216.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RlUix-0007vL-Qp>; Fri, 13 Jan 2012 01:10:28 +0100 Received: by qcse13 with SMTP id e13so1929289qcs.13 for ; Thu, 12 Jan 2012 16:10:26 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:date:message-id:subject:from:to:content-type; bh=D0gIhvzvr0TWxzGXIDu4hMx1GhOUTTZ2UrZ2C2JDFHE=; b=EaksVwS5lvatSIjWqpU+gWjGxGKaYnXY+g80OZXqw+25fOrpMpAyLbeQB84fn9A6lq fzs0b/lI3PbqevfLNjMi5AKW4AEv09ONumcinvouUSPmQ/dhrne49GmXHqIIbGMQQRlD L3GbHKq7hEOPrfQxi57qSEg+8Phd0fzerpLh4= MIME-Version: 1.0 Received: by 10.229.137.79 with SMTP id v15mr37182qct.68.1326413426624; Thu, 12 Jan 2012 16:10:26 -0800 (PST) Received: by 10.224.75.21 with HTTP; Thu, 12 Jan 2012 16:10:26 -0800 (PST) Date: Thu, 12 Jan 2012 16:10:26 -0800 Message-ID: From: Beifang Niu To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=00235452f4901e8bb404b65db177 X-Originating-IP: 209.85.216.182 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326413428-000049E7-2111E717/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.109981, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.2 required=5.0 tests=DNS_FROM_RFC_ABUSE, HTML_40_50, HTML_MESSAGE,HTML_OBFUSCATE_10_20,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] match number of globalalignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 13 Jan 2012 00:10:30 -0000 --00235452f4901e8bb404b65db177 Content-Type: text/plain; charset=ISO-8859-1 Hi all, There is one example for pairwise global alignment http://trac.seqan.de/wiki/Tutorial/Alignments in the seqan tutorial. I can get the alignment output using the example code. I am wondering if there is any metafunction which can be used to get the match number of alignment. If not, how can i get the match number from an alignment result ? thank you, Beifang. --00235452f4901e8bb404b65db177 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all,

There is one= example for pairwise global alignment=A0http://trac.seqan.de/wiki/Tutorial/Alignments= =A0in the=A0seqan=A0tutorial.=A0
I can get the alignment output using the example code. I am wondering = if there is any metafunction which can be used to get the match number of a= lignment.=A0
If not, how can i get the match number from an align= ment result ?

thank you,
Beifang.
--00235452f4901e8bb404b65db177-- From weese@campus.fu-berlin.de Fri Jan 13 07:59:50 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rlb76-0005EO-0O>; Fri, 13 Jan 2012 07:59:48 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rlb75-0006zP-Tl>; Fri, 13 Jan 2012 07:59:47 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rlb75-00076l-NT>; Fri, 13 Jan 2012 07:59:47 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Fri, 13 Jan 2012 07:59:47 +0100 From: "Weese, David" To: SeqAn Development Date: Fri, 13 Jan 2012 07:59:46 +0100 Thread-Topic: [Seqan-dev] match number of globalalignment Thread-Index: AczRwO9jtWAX85J2QNGk72OCpKeWWQ== Message-ID: <3D24FDFF-A2CF-4FCA-949F-DC4378831109@campus.fu-berlin.de> References: In-Reply-To: Accept-Language: de-DE Content-Language: de-DE X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: multipart/alternative; boundary="_000_3D24FDFFA2CF4FCA949FDC4378831109campusfuberlinde_" MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326437988-000049E7-E0F73F16/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.412011, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=ALL_TRUSTED,HTML_50_60, HTML_MESSAGE Subject: Re: [Seqan-dev] match number of globalalignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 13 Jan 2012 06:59:50 -0000 --_000_3D24FDFFA2CF4FCA949FDC4378831109campusfuberlinde_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SGksDQoNCkkgZG9uJ3Qga25vdyB3aGF0IHlvdSBtZWFuIHdpdGggbWF0Y2ggbnVtYmVyLiBJcyB0 aGlzIHRoZSBhbGlnbm1lbnQgc2NvcmUgd2hpY2ggaXMgcmV0dXJuZWQgYnkgZ2xvYmFsQWxpZ24/ DQoNCkNoZWVycw0KRGF2aWQNCg0KVm9uIG1laW5lbSBpUGhvbmUgZ2VzZW5kZXQNCg0KQW0gMTMu MDEuMjAxMiB1bSAwMToxMCBzY2hyaWViICJCZWlmYW5nIE5pdSIgPG5laWxuaXUuY25AZ21haWwu Y29tPG1haWx0bzpuZWlsbml1LmNuQGdtYWlsLmNvbT4+Og0KDQpIaSBhbGwsDQoNClRoZXJlIGlz IG9uZSBleGFtcGxlIGZvciBwYWlyd2lzZSBnbG9iYWwgYWxpZ25tZW50IGh0dHA6Ly90cmFjLnNl cWFuLmRlL3dpa2kvVHV0b3JpYWwvQWxpZ25tZW50cyBpbiB0aGUgc2VxYW4gdHV0b3JpYWwuDQpJ IGNhbiBnZXQgdGhlIGFsaWdubWVudCBvdXRwdXQgdXNpbmcgdGhlIGV4YW1wbGUgY29kZS4gSSBh bSB3b25kZXJpbmcgaWYgdGhlcmUgaXMgYW55IG1ldGFmdW5jdGlvbiB3aGljaCBjYW4gYmUgdXNl ZCB0byBnZXQgdGhlIG1hdGNoIG51bWJlciBvZiBhbGlnbm1lbnQuDQpJZiBub3QsIGhvdyBjYW4g aSBnZXQgdGhlIG1hdGNoIG51bWJlciBmcm9tIGFuIGFsaWdubWVudCByZXN1bHQgPw0KDQp0aGFu ayB5b3UsDQpCZWlmYW5nLg0KX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX18NCnNlcWFuLWRldiBtYWlsaW5nIGxpc3QNCnNlcWFuLWRldkBsaXN0cy5mdS1iZXJs aW4uZGU8bWFpbHRvOnNlcWFuLWRldkBsaXN0cy5mdS1iZXJsaW4uZGU+DQpodHRwczovL2xpc3Rz LmZ1LWJlcmxpbi5kZS9saXN0aW5mby9zZXFhbi1kZXYNCg== --_000_3D24FDFFA2CF4FCA949FDC4378831109campusfuberlinde_ Content-Type: text/html; 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Fri, 13 Jan 2012 20:24:13 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RlmjV-0001ZL-6r>; Fri, 13 Jan 2012 20:24:13 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RlmjV-00022A-18>; Fri, 13 Jan 2012 20:24:13 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Fri, 13 Jan 2012 20:24:12 +0100 From: "Weese, David" To: SeqAn Development Date: Fri, 13 Jan 2012 20:24:12 +0100 Thread-Topic: [Seqan-dev] match number of globalalignment Thread-Index: AczSKO41qPbIyI+BTlmkkTtx8Ps24Q== Message-ID: <498BF161-4C57-4021-BAE7-1E78C339F8A2@fu-berlin.de> References: <3D24FDFF-A2CF-4FCA-949F-DC4378831109@campus.fu-berlin.de> In-Reply-To: <3D24FDFF-A2CF-4FCA-949F-DC4378831109@campus.fu-berlin.de> Accept-Language: de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326482653-000049E7-82F27A2D/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.216566, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] match number of globalalignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 13 Jan 2012 19:24:17 -0000 Hi, You can iterate with two iterators it1, it2 simultaneously over the two row= s of the align object, see Task 1 of http://trac.seqan.de/wiki/Tutorial/Ali= gnments. A match occurs whenever both isGap(it1) and isGap(it2) are false. Simply co= unt them. Regards, David -- David Weese weese@inf.fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75246 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 021=20 Am 13.01.2012 um 20:11 schrieb Beifang Niu: > Hi David, >=20 > One example for match number is the following: >=20 > If I got the alignment using global alignment, the match number is 5.=20 >=20 > AACCGT > | | | | | > AATCGT >=20 > I just can get the alignment using globalalignment but how can I get the = match number of base pairs ? >=20 > thanks, > Beifang. >=20 From manuel.holtgrewe@fu-berlin.de Sat Jan 14 14:17:47 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rm3UP-0001i6-ME>; Sat, 14 Jan 2012 14:17:45 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rm3UP-0002vZ-Jr>; Sat, 14 Jan 2012 14:17:45 +0100 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.100]) by inpost2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtpsa (envelope-from ) id <1Rm3UP-0007NZ-Gt>; Sat, 14 Jan 2012 14:17:45 +0100 Message-ID: <4F118079.4080501@fu-berlin.de> Date: Sat, 14 Jan 2012 14:17:45 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: SeqAn Development References: <3D24FDFF-A2CF-4FCA-949F-DC4378831109@campus.fu-berlin.de> <498BF161-4C57-4021-BAE7-1E78C339F8A2@fu-berlin.de> In-Reply-To: <498BF161-4C57-4021-BAE7-1E78C339F8A2@fu-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326547065-000049E7-0ADF517B/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000016, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] match number of globalalignment X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 14 Jan 2012 13:17:47 -0000 This gives an example http://trac.seqan.de/browser/trunk/seqan/extras/demos/bam_stats.cpp#L196 On 01/13/2012 08:24 PM, Weese, David wrote: > Hi, > > You can iterate with two iterators it1, it2 simultaneously over the two rows of the align object, see Task 1 of http://trac.seqan.de/wiki/Tutorial/Alignments. > A match occurs whenever both isGap(it1) and isGap(it2) are false. Simply count them. > > Regards, > David > > -- > David Weese weese@inf.fu-berlin.de > Freie Universität Berlin http://www.inf.fu-berlin.de/ > Institut für Informatik Phone: +49 30 838 75246 > Takustraße 9 Algorithmic Bioinformatics > 14195 Berlin Room 021 > > Am 13.01.2012 um 20:11 schrieb Beifang Niu: > >> Hi David, >> >> One example for match number is the following: >> >> If I got the alignment using global alignment, the match number is 5. >> >> AACCGT >> | | | | | >> AATCGT >> >> I just can get the alignment using globalalignment but how can I get the match number of base pairs ? >> >> thanks, >> Beifang. >> > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From manuel.holtgrewe@fu-berlin.de Tue Jan 17 22:57:37 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RnH28-0007g2-4g>; Tue, 17 Jan 2012 22:57:36 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1RnH28-00023w-1j>; Tue, 17 Jan 2012 22:57:36 +0100 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.100]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RnH27-0007RN-Uh>; Tue, 17 Jan 2012 22:57:36 +0100 Message-ID: <4F15EECE.9030702@fu-berlin.de> Date: Tue, 17 Jan 2012 22:57:34 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:8.0) Gecko/20111124 Thunderbird/8.0 MIME-Version: 1.0 To: "k.okonechnikov@gmail.com" , SeqAn Development References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326837456-000049E7-D0CB1A7A/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.139778, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] small patch for CommandLineParser X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 17 Jan 2012 21:57:37 -0000 Konstantin, thank you for your patch! However, I believe that applying the patch to the SeqAn code base leads to more work that is probably not justified right now. We might incorporate the behaviour from your patch in a future (revamped) version of the command line parser. Let me explain: Currently, all programs expect the old behaviour and print a banner and the short help on their own after the error message. This makes the error message disappear before the large short help. We plan to rewrite the command line parser in the near future and thus I do not want to adjust all applications to this patch and then shortly afterwards to the new command line parser interface. I will forward your proposal to the people responsible for the new command line parser and ask them to consider this behaviour in the new code. Again, thanks for the effort of creating and sending in the patch, we appreciate it and hope to incorporate your and other user's further improvements into the library. Bests, Manuel On 01/12/2012 03:00 PM, Konstantin Okonechnikov wrote: > Hi! > The patch file is attached. > > The patch feature: show an error message when the required number of > command line parameters doesn't match the number of given parameters. > > Best regards, > Konstantin From lmanchon@univ-montp2.fr Tue Jan 17 23:02:00 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RnH6N-0007nz-4d>; Tue, 17 Jan 2012 23:01:59 +0100 Received: from mailhub-out2.univ-montp2.fr ([162.38.101.224]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RnH6M-0002ZA-VU>; Tue, 17 Jan 2012 23:01:59 +0100 Received: from [162.38.194.43] ([162.38.194.43]) (authenticated bits=0) by mailhub-out2.univ-montp2.fr (8.14.3/8.14.3) with ESMTP id q0HM1tvc022531 (version=TLSv1/SSLv3 cipher=AES256-SHA bits=256 verify=NO) for ; Tue, 17 Jan 2012 23:01:56 +0100 Message-ID: <4F15EFD1.105@univ-montp2.fr> Date: Tue, 17 Jan 2012 23:01:53 +0100 From: Laurent MANCHON Organization: SKT User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; fr; rv:1.9.2.25) Gecko/20111213 Lightning/1.0b2 Thunderbird/3.1.17 MIME-Version: 1.0 To: SeqAn Development Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: clamav-milter 0.97 at mailhub-out2.univ-montp2.fr X-Virus-Status: Clean X-Originating-IP: 162.38.101.224 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1326837719-000049E7-3FE6204D/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.156489, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, PLING_QUERY,UPPERCASE_25_50 Subject: [Seqan-dev] Fwd: Re: bug ?! X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: lmanchon@um2.fr, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 17 Jan 2012 22:02:00 -0000 --Hi, is anyone able to fix the bug in the FAR software developed by Matthias Dodt FAR? thank you -- Hi Laurent! Sorry for the delay in reply. Yes you are right, there is a bug in the software. Unfortunately i cannot fix this at the moment since i have moved out of sience several month ago. I contacted my group but currently there seems to be nobody taking care of this. I think it will be fixed in the future, but i can't tell you when. I will get back to you if i have further information. thanks, mat 2012/1/6 laurent manchon: > --hello, > > i have some problem to clean my sequences using this adaptor string: > AATCTCGTATGCCGTCTTCTGCTTGC > > this is my input file: >>sequence_100104 > ATAGTCAACGGCTGAGGATTTGGCATCTCGTA >>sequence_100105 > ATAGTCAAGATAGAGCTACTGGAGAATCTCGA >>sequence_100106 > ATAGTCAAGATAGAGCTACTGGAGAATCTCGT >>sequence_100107 > ATAGTCAAGATAGAGCTACTGGGGAATCTCGT > > > i use this command to clean: > > far --source reads.fa --target reads_no_adapters.fa --adapters myAdapters.fa --format > fasta --cut-off 4 --min-overlap 2 --min-readlength 16 --trim-end right > > and this is the output: > >>sequence_100104 > ATAGTCAACGGCTGAGGATTTGGCATCTCGTA >>sequence_100105 > ATAGTCAAGATAGAGCTACTGGAGAATCTCGA >>sequence_100106 > ATAGTCAAGATAGAGCTACTGGAG >>sequence_100107 > ATAGTCAAGATAGAGCTACTGGGG > > > So, sequence_100106 and sequence_100107 are well cleaned but not > sequence_100104, the good results should be: > >>sequence_100104 > ATAGTCAACGGCTGAGGATTTGGC >>sequence_100105 > ATAGTCAAGATAGAGCTACTGGAGAATCTCGA >>sequence_100106 > ATAGTCAAGATAGAGCTACTGGAG >>sequence_100107 > ATAGTCAAGATAGAGCTACTGGGG > > substring \"ATCTCGTA\" is a part of adaptor sequence ! > > Somebody has a solution to resolve this problem ? > > thank you. > > > > > > > > -- > This message was sent to your SourceForge.net email alias via the web mail form. You may reply to this message directly, or via https://sourceforge.net/sendmessage.php?touser=2041456 > To update your email alias preferences, please visit https://sourceforge.net/account From leisuncumt@yahoo.com Thu Jan 26 09:14:55 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RqKTu-0002Ib-1w>; Thu, 26 Jan 2012 09:14:54 +0100 Received: from nm3.bullet.mail.sp2.yahoo.com ([98.139.91.73]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with smtp (envelope-from ) id <1RqKTt-0004Uz-Jc>; Thu, 26 Jan 2012 09:14:54 +0100 Received: from [98.139.91.62] by nm3.bullet.mail.sp2.yahoo.com with NNFMP; 26 Jan 2012 08:14:52 -0000 Received: from [98.139.91.51] by tm2.bullet.mail.sp2.yahoo.com with NNFMP; 26 Jan 2012 08:14:52 -0000 Received: from [127.0.0.1] by omp1051.mail.sp2.yahoo.com with NNFMP; 26 Jan 2012 08:14:52 -0000 X-Yahoo-Newman-Property: ymail-3 X-Yahoo-Newman-Id: 138471.2412.bm@omp1051.mail.sp2.yahoo.com Received: (qmail 8040 invoked by uid 60001); 26 Jan 2012 08:14:51 -0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=yahoo.com; s=s1024; t=1327565691; bh=e0pxjeUu5w2NulIwsb57kj1qOm8hVfShUgjpqBLadsU=; h=X-YMail-OSG:Received:X-Mailer:Message-ID:Date:From:Reply-To:Subject:To:MIME-Version:Content-Type; b=WAaG2aBP2ZJKmPvRUb+B/XH5iZI4hddGeI0CCEcwffP7fN9oeW0PrYCjZKqNJF3qqcmdO/2DdBzq/32b69yFQ4FKQPZrWmBMhRGJPhhfIRXbPhLfT91rM0w1oHMhSSnqgOUu1Jo3q0eE7DZ1GuT/vLvOsYejH12H7E7JxLmz7+g= DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=X-YMail-OSG:Received:X-Mailer:Message-ID:Date:From:Reply-To:Subject:To:MIME-Version:Content-Type; b=lc4ysUXYiFRyJO1QwF6KWV/PqBdGOV8KKjnfB48w7Iy++AY3puhTjhAsfrISfbHs7KtqeDFgEbJrv+6E4ojeMupgyze1CzweSmhavDGY+K2YHa1x4D8MtBO1IcsrwsNFFj6y8iMA7soaMQXAqxgH1YzCHZtc5qq28FDbDPDYR84=; X-YMail-OSG: KzRBIfMVM1ksBLXYEW15T0c9oDau8oFAvV13La0mHOLPop_ kXXOIUQvJ5_B5_CWuZf03sXRH61qLNSCed1_JLXZAfAg3QSJjw1bBGJZMeHG 3XA0Rxm0weplR.Mm7WEoS5IrTHoTLdZhfCyHrYw4Ncw_mrKPp3KBgONDr1GG y_l_ymeBztZRTS3qNHGgEE3HdF_g._wegIejyyb8BbZgH4dqvJmmGscyG8o2 JwHhMMkIwAKbxhSExF1IqcVbJVoL9ryj_1YCRXl2n9JNEP04b88vDpEaFecU 1WjXCxs8lXORbV7hUXCe3BoFDqssNzWvO1ulUSgooF0003ZYZuVnaZw1FFUl CV8LykYgluICpk0_fEL.IAWO3ACivXJCdZWfsYxeHawyOfisX15P7zKQLg22 ehXoEGQc5UWXC8aDnjUzUgyhFXq3NGmtnkA-- Received: from [123.243.149.212] by web111617.mail.gq1.yahoo.com via HTTP; Thu, 26 Jan 2012 00:14:51 PST X-Mailer: YahooMailWebService/0.8.116.331537 Message-ID: <1327565691.7916.YahooMailNeo@web111617.mail.gq1.yahoo.com> Date: Thu, 26 Jan 2012 00:14:51 -0800 (PST) From: Lei Sun To: "seqan-dev@lists.fu-berlin.de" MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="-732675353-1349963925-1327565691=:7916" X-Originating-IP: 98.139.91.73 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327565694-000049E7-042F6717/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000019, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: xx X-Spam-Status: No, score=2.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,HTML_90_100,HTML_MESSAGE,TO_ADDRESS_EQ_REAL Subject: [Seqan-dev] seqan checkout problem X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: Lei Sun , SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 26 Jan 2012 08:14:55 -0000 ---732675353-1349963925-1327565691=:7916 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi,=0A=0AI tried to checkout seqan through SVN but an error was shown like= =0A=0A"svn: Can't find a temporary directory: Internal error"=0A=0ABTW, I f= ailed using either Eclipse or Tortoise on Windows, SVN or Eclipse on linux.= =A0=0A=0A=0A=0ACheers,=0A=0ALei=A0=0A ---732675353-1349963925-1327565691=:7916 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,

I tried to checkout seqan through SVN but an error was= shown like

"svn: Can't find = a temporary directory: Internal error"

BTW, I failed using either Eclipse or Tortoise on Windows, SVN or E= clipse on linux. 



Cheers,

Lei 
---732675353-1349963925-1327565691=:7916-- From manuel.holtgrewe@fu-berlin.de Thu Jan 26 18:30:15 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RqT9L-0005Ed-4t>; Thu, 26 Jan 2012 18:30:15 +0100 Received: from inpost2.zedat.fu-berlin.de ([130.133.4.69]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1RqT9L-00082p-09>; Thu, 26 Jan 2012 18:30:15 +0100 Received: from 91-65-212-104-dynip.superkabel.de ([91.65.212.104] helo=[192.168.0.100]) by inpost2.zedat.fu-berlin.de (Exim 4.69) with esmtpsa (envelope-from ) id <1RqT9K-0006fI-TM>; Thu, 26 Jan 2012 18:30:14 +0100 Message-ID: <4F218DA6.1030903@fu-berlin.de> Date: Thu, 26 Jan 2012 18:30:14 +0100 From: Manuel Holtgrewe User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:9.0) Gecko/20111229 Thunderbird/9.0 MIME-Version: 1.0 To: Lei Sun , SeqAn Development References: <1327565691.7916.YahooMailNeo@web111617.mail.gq1.yahoo.com> In-Reply-To: <1327565691.7916.YahooMailNeo@web111617.mail.gq1.yahoo.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Originating-IP: 91.65.212.104 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327599015-000049E7-32AEC6E2/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000380, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] seqan checkout problem X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 26 Jan 2012 17:30:16 -0000 Lei Sun, thanks for reporting this. It should be fixed by now. *m On 01/26/2012 09:14 AM, Lei Sun wrote: > Hi, > > I tried to checkout seqan through SVN but an error was shown like > > "svn: Can't find a temporary directory: Internal error" > > BTW, I failed using either Eclipse or Tortoise on Windows, SVN or > Eclipse on linux. > > > > Cheers, > > Lei From jer15@hermes.cam.ac.uk Fri Jan 27 15:10:19 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RqmVP-00033Z-5b>; Fri, 27 Jan 2012 15:10:19 +0100 Received: from ppsw-51.csi.cam.ac.uk ([131.111.8.151]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RqmVP-0003Li-1u>; Fri, 27 Jan 2012 15:10:19 +0100 X-Cam-AntiVirus: no malware found X-Cam-SpamDetails: not scanned X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from wifi-host-78.mrc-bsu.cam.ac.uk ([193.60.87.78]:55471) by ppsw-51.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.158]:587) with esmtpsa (PLAIN:jer15) (TLSv1:DHE-RSA-CAMELLIA256-SHA:256) id 1RqmVO-0000Gz-YW (Exim 4.72) for seqan-dev@lists.fu-berlin.de (return-path ); Fri, 27 Jan 2012 14:10:18 +0000 Message-ID: <4F22B04A.6060003@mail.cryst.bbk.ac.uk> Date: Fri, 27 Jan 2012 14:10:18 +0000 From: John Reid User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:9.0) Gecko/20111229 Thunderbird/9.0 MIME-Version: 1.0 To: SeqAn Development Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: "J.E. Reid" X-Originating-IP: 131.111.8.151 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327673419-000049E7-A7F5F0FA/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.296321, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.0 required=5.0 tests=none Subject: [Seqan-dev] PISA toolbox code X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 27 Jan 2012 14:10:20 -0000 Hi, I've recently become interested in variable order Markov chains. I plan to develop some algorithms that extend and use these chains. I've been using the SeqAn library for a while now and I wonder if there are any plans to release the source code for the PISA toolbox. Regards, John Reid. From mekentosj@gmail.com Mon Jan 30 00:37:50 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RreJg-00038r-Lj>; Mon, 30 Jan 2012 00:37:48 +0100 Received: from mail-we0-f182.google.com ([74.125.82.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RreJg-00074b-I5>; Mon, 30 Jan 2012 00:37:48 +0100 Received: by werm13 with SMTP id m13so1931447wer.13 for ; Sun, 29 Jan 2012 15:37:48 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:date:message-id:subject:from:to:content-type :content-transfer-encoding; bh=C649uFioEaagnV0YyF5Cs805UlY9lqgJtGRxbVyYZNs=; b=mJGz88H+zhJz60PvzG8ciCqZWM5lD3PGQCK45ir+54Qp1Z7pf4ohU51miYRrkVxVir qvbWOcMn7Dv2XWV+tFv0C2iVHmt2L1tDBOvaSjwzIzzCppLmKbjIsxpGXk/nT1SRZKCZ az44+kuVLYwZltwZMhILKquhb7v9PiqQsCa38= MIME-Version: 1.0 Received: by 10.216.132.195 with SMTP id o45mr6050508wei.17.1327880268272; Sun, 29 Jan 2012 15:37:48 -0800 (PST) Received: by 10.180.77.133 with HTTP; Sun, 29 Jan 2012 15:37:48 -0800 (PST) Date: Sun, 29 Jan 2012 23:37:48 +0000 Message-ID: From: Alexander Griekspoor To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable X-Originating-IP: 74.125.82.182 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327880268-000049E7-C9DD14F0/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000004, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS Subject: [Seqan-dev] Using seqan in stock Xcode project X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 29 Jan 2012 23:37:50 -0000 Hi everybody, We're currently evaluating whether to use seqan in one or more of our projects, at first glance it looks awesome! I'm trying to get it to work in a stock Cocoa application Xcode project but am bumping into a number of errors being spit out. I'd ideally like to use it in a 32/64bit universal app. Two screenshots: https://mekentosj-private.s3.amazonaws.com/seqan1.png https://mekentosj-private.s3.amazonaws.com/seqan2.png And the simple test app: https://mekentosj-private.s3.amazonaws.com/SeqanTest.zip Any clues how to set this up? Many thanks! Alex --=20 **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 ** Alexander Griekspoor=C2=A0 PhD ** **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj.co= m =C2=A0Papers - Your Personal Library of Science =C2=A0 =C2=A0=C2=A0 Winner of the Apple Design Awards =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 available wherever you go: =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers/ipad **************************************************** From mekentosj@gmail.com Mon Jan 30 00:48:34 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RreU3-0003Tj-Cy>; Mon, 30 Jan 2012 00:48:32 +0100 Received: from mail-ww0-f50.google.com ([74.125.82.50]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RreU3-00081Q-6w>; Mon, 30 Jan 2012 00:48:31 +0100 Received: by wgbdr11 with SMTP id dr11so3813407wgb.31 for ; Sun, 29 Jan 2012 15:48:30 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type:content-transfer-encoding; bh=uWrzC5WEPRn6TnDucZcf1ZtoYC1fvIiKkfchBx2AnMI=; b=ABfhHZPkI/yp1/zfPS1ftw3CuXFaHpVUbQSmEsxc9DyKghXu2QHTAZ3tDoKibIitzW bzL0IRE3JUkkahvAm0JWeJaelyKgtJykGXG07njjrmJAMwjSWyEbI2WZjj/VCVwGFTp/ ZFad1VtrNmGnwP9g5B0EHJSwavif5pHdjDM1E= MIME-Version: 1.0 Received: by 10.180.107.34 with SMTP id gz2mr20527510wib.21.1327880910098; Sun, 29 Jan 2012 15:48:30 -0800 (PST) Received: by 10.180.77.133 with HTTP; Sun, 29 Jan 2012 15:48:30 -0800 (PST) In-Reply-To: References: Date: Sun, 29 Jan 2012 23:48:30 +0000 Message-ID: From: Alexander Griekspoor To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable X-Originating-IP: 74.125.82.50 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327880911-000049E7-A217B2C6/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] Using seqan in stock Xcode project X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 29 Jan 2012 23:48:34 -0000 To follow up on my last email, the warnings shown while building with the LLVM/GCC4.2 compiler setting. If I try with the LLVM3.0 option (which would be preferred I guess) I get the following errors: https://mekentosj-private.s3.amazonaws.com/seqan3.png https://mekentosj-private.s3.amazonaws.com/seqan4.png it seems to struggle over the same file/lines. I did see this article: http://trac.seqan.de/wiki/HowTo/UseLatestClangInXcode#HowTo:UsethelatestLLV= MClanginXcode but it seems outdates since Xcode moved to LLVM 3.0 with C++ support in the mean time. Hope you have a way to get things going. Alex On Sun, Jan 29, 2012 at 11:37 PM, Alexander Griekspoor wrote: > Hi everybody, > > We're currently evaluating whether to use seqan in one or more of our > projects, at first glance it looks awesome! > I'm trying to get it to work in a stock Cocoa application Xcode > project but am bumping into a number of errors being spit out. > I'd ideally like to use it in a 32/64bit universal app. > > Two screenshots: > https://mekentosj-private.s3.amazonaws.com/seqan1.png > https://mekentosj-private.s3.amazonaws.com/seqan2.png > > And the simple test app: > https://mekentosj-private.s3.amazonaws.com/SeqanTest.zip > > Any clues how to set this up? > Many thanks! > Alex > > > > -- > **************************************************** > =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 ** Alexander Griekspoor=C2=A0 PhD ** > **************************************************** > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj.= com > > =C2=A0Papers - Your Personal Library of Science > =C2=A0 =C2=A0=C2=A0 Winner of the Apple Design Awards > =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution > =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers > > =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 available wherever you go: > =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers/ipad > **************************************************** --=20 **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 ** Alexander Griekspoor=C2=A0 PhD ** **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj.co= m =C2=A0Papers - Your Personal Library of Science =C2=A0 =C2=A0=C2=A0 Winner of the Apple Design Awards =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 available wherever you go: =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers/ipad **************************************************** From weese@campus.fu-berlin.de Mon Jan 30 19:25:30 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rrvuz-0006Rm-1a>; Mon, 30 Jan 2012 19:25:29 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rrvuy-00053v-VA>; Mon, 30 Jan 2012 19:25:29 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rrvuy-00072S-Og>; Mon, 30 Jan 2012 19:25:28 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 30 Jan 2012 19:25:28 +0100 From: "Weese, David" To: SeqAn Development Date: Mon, 30 Jan 2012 19:25:26 +0100 Thread-Topic: [Seqan-dev] Using seqan in stock Xcode project Thread-Index: AczffIpYuI30P3PtTO6HStgdd0X04A== Message-ID: References: In-Reply-To: Accept-Language: de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327947929-000049E7-8682854B/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000650, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Using seqan in stock Xcode project X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 30 Jan 2012 18:25:31 -0000 Hi Alex, I have no explanation for these errors. Have you created your Xcode project= with CMake? This should compile flawlessly on OS X Lion with LLVM 3.0 and = also GCC 4.2. Maybe you do and compare the compilation fags of the two proj= ect files. You can ignore the wiki page you have found. It describes how to use LLVM 3= .0 under Snow Leopard. Regards, David Am 30.01.2012 um 00:48 schrieb Alexander Griekspoor: > To follow up on my last email, the warnings shown while building with > the LLVM/GCC4.2 compiler setting. If I try with the LLVM3.0 option > (which would be preferred I guess) I get the following errors: >=20 > https://mekentosj-private.s3.amazonaws.com/seqan3.png > https://mekentosj-private.s3.amazonaws.com/seqan4.png >=20 > it seems to struggle over the same file/lines. >=20 > I did see this article: >=20 > http://trac.seqan.de/wiki/HowTo/UseLatestClangInXcode#HowTo:UsethelatestL= LVMClanginXcode >=20 > but it seems outdates since Xcode moved to LLVM 3.0 with C++ support > in the mean time. > Hope you have a way to get things going. > Alex >=20 > On Sun, Jan 29, 2012 at 11:37 PM, Alexander Griekspoor > wrote: >> Hi everybody, >>=20 >> We're currently evaluating whether to use seqan in one or more of our >> projects, at first glance it looks awesome! >> I'm trying to get it to work in a stock Cocoa application Xcode >> project but am bumping into a number of errors being spit out. >> I'd ideally like to use it in a 32/64bit universal app. >>=20 >> Two screenshots: >> https://mekentosj-private.s3.amazonaws.com/seqan1.png >> https://mekentosj-private.s3.amazonaws.com/seqan2.png >>=20 >> And the simple test app: >> https://mekentosj-private.s3.amazonaws.com/SeqanTest.zip >>=20 >> Any clues how to set this up? >> Many thanks! >> Alex >>=20 >>=20 >>=20 >> -- >> **************************************************** >> ** Alexander Griekspoor PhD ** >> **************************************************** >> mekentosj.com >>=20 >> Papers - Your Personal Library of Science >> Winner of the Apple Design Awards >> Best Mac OS X Scientific Solution >> http://mekentosj.com/papers >>=20 >> Papers for iPad - all your papers >> available wherever you go: >> http://mekentosj.com/papers/ipad >> **************************************************** >=20 >=20 >=20 > --=20 > **************************************************** > ** Alexander Griekspoor PhD ** > **************************************************** > mekentosj.com >=20 > Papers - Your Personal Library of Science > Winner of the Apple Design Awards > Best Mac OS X Scientific Solution > http://mekentosj.com/papers >=20 > Papers for iPad - all your papers > available wherever you go: > http://mekentosj.com/papers/ipad > **************************************************** >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From mekentosj@gmail.com Mon Jan 30 20:04:08 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RrwWM-0007cG-AL>; Mon, 30 Jan 2012 20:04:06 +0100 Received: from mail-wi0-f182.google.com ([209.85.212.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RrwWM-0004dD-5x>; Mon, 30 Jan 2012 20:04:06 +0100 Received: by wibhn14 with SMTP id hn14so5445272wib.13 for ; Mon, 30 Jan 2012 11:04:05 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type:content-transfer-encoding; bh=nqbqhHTS4eB83AL9hej85m/jj4u2R9G3rLMqMLaScJ4=; b=A63dLFjncoXNuiJDeAnvYR0n8co1DCuPKQpyceI5vDxfK1ISkoarsnACuEd36+/Fmr bYETKCCSirhuOdmAMW1/3f0Iqz3ZpqTUSs1+V8Comof+pZEJgnKF/c3ysoPIRoUv2RHn FTZE+whEs7nk5TXDXSnSgk5FNbXy1YtvqyXqk= MIME-Version: 1.0 Received: by 10.180.77.200 with SMTP id u8mr29443622wiw.18.1327950245846; Mon, 30 Jan 2012 11:04:05 -0800 (PST) Received: by 10.180.77.133 with HTTP; Mon, 30 Jan 2012 11:04:05 -0800 (PST) In-Reply-To: References: Date: Mon, 30 Jan 2012 19:04:05 +0000 Message-ID: From: Alexander Griekspoor To: SeqAn Development Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable X-Originating-IP: 209.85.212.182 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327950246-000049E7-086A87B2/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] Using seqan in stock Xcode project X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 30 Jan 2012 19:04:08 -0000 Hi David, No, I have created a plain vanilla project using File -> New Project, then added the headers from the 1.3 release download. I wanted to avoid having to use CMake or the Xcode project it produces that contains all the 136 seqAn targets. I figured it should be one of the build settings. Would you or anyone have an example Xcode project that is setup in the way I described or an Xcode project that works for comparison purposes? Many thanks, Alex On Mon, Jan 30, 2012 at 6:25 PM, Weese, David w= rote: > Hi Alex, > > I have no explanation for these errors. Have you created your Xcode proje= ct with CMake? This should compile flawlessly on OS X Lion with LLVM 3.0 an= d also GCC 4.2. Maybe you do and compare the compilation fags of the two pr= oject files. > > You can ignore the wiki page you have found. It describes how to use LLVM= 3.0 under Snow Leopard. > > Regards, > David > > Am 30.01.2012 um 00:48 schrieb Alexander Griekspoor: > >> To follow up on my last email, the warnings shown while building with >> the LLVM/GCC4.2 compiler setting. If I try with the LLVM3.0 option >> (which would be preferred I guess) I get the following errors: >> >> https://mekentosj-private.s3.amazonaws.com/seqan3.png >> https://mekentosj-private.s3.amazonaws.com/seqan4.png >> >> it seems to struggle over the same file/lines. >> >> I did see this article: >> >> http://trac.seqan.de/wiki/HowTo/UseLatestClangInXcode#HowTo:Usethelatest= LLVMClanginXcode >> >> but it seems outdates since Xcode moved to LLVM 3.0 with C++ support >> in the mean time. >> Hope you have a way to get things going. >> Alex >> >> On Sun, Jan 29, 2012 at 11:37 PM, Alexander Griekspoor >> wrote: >>> Hi everybody, >>> >>> We're currently evaluating whether to use seqan in one or more of our >>> projects, at first glance it looks awesome! >>> I'm trying to get it to work in a stock Cocoa application Xcode >>> project but am bumping into a number of errors being spit out. >>> I'd ideally like to use it in a 32/64bit universal app. >>> >>> Two screenshots: >>> https://mekentosj-private.s3.amazonaws.com/seqan1.png >>> https://mekentosj-private.s3.amazonaws.com/seqan2.png >>> >>> And the simple test app: >>> https://mekentosj-private.s3.amazonaws.com/SeqanTest.zip >>> >>> Any clues how to set this up? >>> Many thanks! >>> Alex >>> >>> >>> >>> -- >>> **************************************************** >>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0** Alexander Griekspoor =C2=A0PhD ** >>> **************************************************** >>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentos= j.com >>> >>> =C2=A0Papers - Your Personal Library of Science >>> =C2=A0 =C2=A0 =C2=A0Winner of the Apple Design Awards >>> =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution >>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers >>> >>> =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers >>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0available wherever you go: >>> =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers/ipad >>> **************************************************** >> >> >> >> -- >> **************************************************** >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0** Alexander Griekspoor =C2=A0PhD ** >> **************************************************** >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj= .com >> >> =C2=A0Papers - Your Personal Library of Science >> =C2=A0 =C2=A0 =C2=A0Winner of the Apple Design Awards >> =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers >> >> =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0available wherever you go: >> =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers/ipad >> **************************************************** >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --=20 **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 ** Alexander Griekspoor=C2=A0 PhD ** **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj.co= m =C2=A0Papers - Your Personal Library of Science =C2=A0 =C2=A0=C2=A0 Winner of the Apple Design Awards =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 available wherever you go: =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers/ipad **************************************************** From weese@campus.fu-berlin.de Mon Jan 30 20:05:05 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RrwXH-0007eP-Va>; Mon, 30 Jan 2012 20:05:04 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RrwXH-0001tC-Ta>; Mon, 30 Jan 2012 20:05:03 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RrwXH-0000v9-O8>; Mon, 30 Jan 2012 20:05:03 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 30 Jan 2012 20:05:03 +0100 From: "Weese, David" To: SeqAn Development Date: Mon, 30 Jan 2012 20:05:03 +0100 Thread-Topic: [Seqan-dev] Using seqan in stock Xcode project Thread-Index: AczfghI1PoYRCL6fQp2PODP9XRDYwA== Message-ID: <396DD682-9AEB-4CF5-A9AA-CA1DCD6CB21C@campus.fu-berlin.de> References: In-Reply-To: Accept-Language: de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327950303-000049E7-92D3AFBA/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000403, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Using seqan in stock Xcode project X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 30 Jan 2012 19:05:05 -0000 Hi again, I forgot to mention that in general it is possible to use SeqAn in a Cocoa = application. I successfully created a (very) simple SAM Viewer for Mac OS X= that allows you to scroll through a multiple read alignment. It simply was= a proof of concept. I started with a fresh Cocoa application and added the core/include and ext= ras/include paths. It is also necessary to let cmake create these ..._gener= ated_forwards.h headers. This can be done by creating a makefile (or Xcode)= project with cmake and compile an arbitrary app, e.g. make alignment (see = "Getting started" in the Wiki). The forwards are generated in core/include = and extras/include below the CMakeCache.txt directory and needs to be added= to the GCC search path also. For me the include paths are: seqan-trunk/core/include/ seqan-trunk/extras/include/ seqan-trunk/build/core/include/ seqan-trunk/build/extras/include/ were created forwards via: cd seqan-trunk mkdir build; cd build cmake .. -G "Unix Makefiles" make alignment I just tried to recompile my Cocoa app and it works flawlessly under Snow L= eopard, GCC 4.2 and the svn trunk. Tomorrow I check whether it works under = Lion also. Hope that helps. Cheers, Dave Am 30.01.2012 um 00:37 schrieb Alexander Griekspoor: > Hi everybody, >=20 > We're currently evaluating whether to use seqan in one or more of our > projects, at first glance it looks awesome! > I'm trying to get it to work in a stock Cocoa application Xcode > project but am bumping into a number of errors being spit out. > I'd ideally like to use it in a 32/64bit universal app. >=20 > Two screenshots: > https://mekentosj-private.s3.amazonaws.com/seqan1.png > https://mekentosj-private.s3.amazonaws.com/seqan2.png >=20 > And the simple test app: > https://mekentosj-private.s3.amazonaws.com/SeqanTest.zip >=20 > Any clues how to set this up? > Many thanks! > Alex >=20 >=20 >=20 > --=20 > **************************************************** > ** Alexander Griekspoor PhD ** > **************************************************** > mekentosj.com >=20 > Papers - Your Personal Library of Science > Winner of the Apple Design Awards > Best Mac OS X Scientific Solution > http://mekentosj.com/papers >=20 > Papers for iPad - all your papers > available wherever you go: > http://mekentosj.com/papers/ipad > **************************************************** >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From mekentosj@gmail.com Mon Jan 30 20:16:29 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RrwiI-0007yH-FP>; Mon, 30 Jan 2012 20:16:26 +0100 Received: from mail-ww0-f50.google.com ([74.125.82.50]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1RrwiI-0005wL-C3>; Mon, 30 Jan 2012 20:16:26 +0100 Received: by wgbdr11 with SMTP id dr11so4849361wgb.31 for ; Mon, 30 Jan 2012 11:16:26 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type:content-transfer-encoding; bh=mswUUclrizfNcn9pp8Ao/iAIO7pOBPUlLVdcdmi3IpY=; b=dtq0Th7WpbGgM+8AIkbhQWqDyOwFu+z/W2QSCDwvuP4zRpPuXyOdiHDxrVUkg+8BvP awNrS8IXpJ46AQBkhCqzWudrBwWIzZTX+g4Ljw87Nl3geNfW8ZG8h65JgMvxQZCRh9iY aZwXfGvu/hMUy4mFcYDNmpTb4EbbuLNrmwXYU= MIME-Version: 1.0 Received: by 10.180.77.200 with SMTP id u8mr29507223wiw.18.1327950986124; Mon, 30 Jan 2012 11:16:26 -0800 (PST) Received: by 10.180.77.133 with HTTP; Mon, 30 Jan 2012 11:16:24 -0800 (PST) In-Reply-To: <396DD682-9AEB-4CF5-A9AA-CA1DCD6CB21C@campus.fu-berlin.de> References: <396DD682-9AEB-4CF5-A9AA-CA1DCD6CB21C@campus.fu-berlin.de> Date: Mon, 30 Jan 2012 19:16:24 +0000 Message-ID: From: Alexander Griekspoor To: SeqAn Development Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable X-Originating-IP: 74.125.82.50 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327950986-000049E7-FF7B74B9/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] Using seqan in stock Xcode project X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 30 Jan 2012 19:16:29 -0000 Ok cool, will give that another try tonight and will let you know if I get it to work. Thanks, Alex On Mon, Jan 30, 2012 at 7:05 PM, Weese, David w= rote: > Hi again, > > I forgot to mention that in general it is possible to use SeqAn in a Coco= a application. I successfully created a (very) simple SAM Viewer for Mac OS= X that allows you to scroll through a multiple read alignment. It simply w= as a proof of concept. > I started with a fresh Cocoa application and added the core/include and e= xtras/include paths. It is also necessary to let cmake create these ..._gen= erated_forwards.h headers. This can be done by creating a makefile (or Xcod= e) project with cmake and compile an arbitrary app, e.g. make alignment (se= e "Getting started" in the Wiki). The forwards are generated in core/includ= e and extras/include below the CMakeCache.txt directory and needs to be add= ed to the GCC search path also. For me the include paths are: > > seqan-trunk/core/include/ > seqan-trunk/extras/include/ > seqan-trunk/build/core/include/ > seqan-trunk/build/extras/include/ > > were created forwards via: > > cd seqan-trunk > mkdir build; cd build > cmake .. -G "Unix Makefiles" > make alignment > > I just tried to recompile my Cocoa app and it works flawlessly under Snow= Leopard, GCC 4.2 and the svn trunk. Tomorrow I check whether it works unde= r Lion also. > > Hope that helps. > > Cheers, > Dave > > Am 30.01.2012 um 00:37 schrieb Alexander Griekspoor: > >> Hi everybody, >> >> We're currently evaluating whether to use seqan in one or more of our >> projects, at first glance it looks awesome! >> I'm trying to get it to work in a stock Cocoa application Xcode >> project but am bumping into a number of errors being spit out. >> I'd ideally like to use it in a 32/64bit universal app. >> >> Two screenshots: >> https://mekentosj-private.s3.amazonaws.com/seqan1.png >> https://mekentosj-private.s3.amazonaws.com/seqan2.png >> >> And the simple test app: >> https://mekentosj-private.s3.amazonaws.com/SeqanTest.zip >> >> Any clues how to set this up? >> Many thanks! >> Alex >> >> >> >> -- >> **************************************************** >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0** Alexander Griekspoor =C2=A0PhD ** >> **************************************************** >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj= .com >> >> =C2=A0Papers - Your Personal Library of Science >> =C2=A0 =C2=A0 =C2=A0Winner of the Apple Design Awards >> =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers >> >> =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0available wherever you go: >> =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers/ipad >> **************************************************** >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --=20 **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 ** Alexander Griekspoor=C2=A0 PhD ** **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj.co= m =C2=A0Papers - Your Personal Library of Science =C2=A0 =C2=A0=C2=A0 Winner of the Apple Design Awards =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 available wherever you go: =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers/ipad **************************************************** From weese@campus.fu-berlin.de Mon Jan 30 20:20:12 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rrwlt-00085N-2L>; Mon, 30 Jan 2012 20:20:09 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rrwlt-0003mF-0I>; Mon, 30 Jan 2012 20:20:09 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rrwls-0001mn-Qo>; Mon, 30 Jan 2012 20:20:08 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Mon, 30 Jan 2012 20:20:08 +0100 From: "Weese, David" To: SeqAn Development Date: Mon, 30 Jan 2012 20:20:07 +0100 Thread-Topic: [Seqan-dev] Using seqan in stock Xcode project Thread-Index: AczfhC2bVL7oVabaRsmd4qXOC+0icw== Message-ID: <286597EF-C118-4E12-947E-AAD31A024F5D@campus.fu-berlin.de> References: In-Reply-To: Accept-Language: de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327951209-000049E7-29CB0F3F/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000003, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Using seqan in stock Xcode project X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 30 Jan 2012 19:20:13 -0000 Ah, you are using the release version of Seqan. That would explain some iss= ues, as I had to rename some identifiers, e.g. id, before Seqan could be us= ed with Objective C. These diffs are not released yet so I suggest you to u= se the svn trunk for now. The diffs are: http://trac.seqan.de/search?q=3Dobjective+c I can send you my xcode.app file tomorrow after it tested it under Lion. Dave Am 30.01.2012 um 20:04 schrieb Alexander Griekspoor: > Hi David, >=20 > No, I have created a plain vanilla project using File -> New Project, > then added the headers from the 1.3 release download. I wanted to > avoid having to use CMake or the Xcode project it produces that > contains all the 136 seqAn targets. I figured it should be one of the > build settings. Would you or anyone have an example Xcode project that > is setup in the way I described or an Xcode project that works for > comparison purposes? > Many thanks, > Alex >=20 > On Mon, Jan 30, 2012 at 6:25 PM, Weese, David = wrote: >> Hi Alex, >>=20 >> I have no explanation for these errors. Have you created your Xcode proj= ect with CMake? This should compile flawlessly on OS X Lion with LLVM 3.0 a= nd also GCC 4.2. Maybe you do and compare the compilation fags of the two p= roject files. >>=20 >> You can ignore the wiki page you have found. It describes how to use LLV= M 3.0 under Snow Leopard. >>=20 >> Regards, >> David >>=20 >> Am 30.01.2012 um 00:48 schrieb Alexander Griekspoor: >>=20 >>> To follow up on my last email, the warnings shown while building with >>> the LLVM/GCC4.2 compiler setting. If I try with the LLVM3.0 option >>> (which would be preferred I guess) I get the following errors: >>>=20 >>> https://mekentosj-private.s3.amazonaws.com/seqan3.png >>> https://mekentosj-private.s3.amazonaws.com/seqan4.png >>>=20 >>> it seems to struggle over the same file/lines. >>>=20 >>> I did see this article: >>>=20 >>> http://trac.seqan.de/wiki/HowTo/UseLatestClangInXcode#HowTo:Usethelates= tLLVMClanginXcode >>>=20 >>> but it seems outdates since Xcode moved to LLVM 3.0 with C++ support >>> in the mean time. >>> Hope you have a way to get things going. >>> Alex >>>=20 >>> On Sun, Jan 29, 2012 at 11:37 PM, Alexander Griekspoor >>> wrote: >>>> Hi everybody, >>>>=20 >>>> We're currently evaluating whether to use seqan in one or more of our >>>> projects, at first glance it looks awesome! >>>> I'm trying to get it to work in a stock Cocoa application Xcode >>>> project but am bumping into a number of errors being spit out. >>>> I'd ideally like to use it in a 32/64bit universal app. >>>>=20 >>>> Two screenshots: >>>> https://mekentosj-private.s3.amazonaws.com/seqan1.png >>>> https://mekentosj-private.s3.amazonaws.com/seqan2.png >>>>=20 >>>> And the simple test app: >>>> https://mekentosj-private.s3.amazonaws.com/SeqanTest.zip >>>>=20 >>>> Any clues how to set this up? >>>> Many thanks! >>>> Alex >>>>=20 >>>>=20 >>>>=20 >>>> -- >>>> **************************************************** >>>> ** Alexander Griekspoor PhD ** >>>> **************************************************** >>>> mekentosj.com >>>>=20 >>>> Papers - Your Personal Library of Science >>>> Winner of the Apple Design Awards >>>> Best Mac OS X Scientific Solution >>>> http://mekentosj.com/papers >>>>=20 >>>> Papers for iPad - all your papers >>>> available wherever you go: >>>> http://mekentosj.com/papers/ipad >>>> **************************************************** >>>=20 >>>=20 >>>=20 >>> -- >>> **************************************************** >>> ** Alexander Griekspoor PhD ** >>> **************************************************** >>> mekentosj.com >>>=20 >>> Papers - Your Personal Library of Science >>> Winner of the Apple Design Awards >>> Best Mac OS X Scientific Solution >>> http://mekentosj.com/papers >>>=20 >>> Papers for iPad - all your papers >>> available wherever you go: >>> http://mekentosj.com/papers/ipad >>> **************************************************** >>>=20 >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev >>=20 >>=20 >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >=20 >=20 >=20 > --=20 > **************************************************** > ** Alexander Griekspoor PhD ** > **************************************************** > mekentosj.com >=20 > Papers - Your Personal Library of Science > Winner of the Apple Design Awards > Best Mac OS X Scientific Solution > http://mekentosj.com/papers >=20 > Papers for iPad - all your papers > available wherever you go: > http://mekentosj.com/papers/ipad > **************************************************** >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From mekentosj@gmail.com Mon Jan 30 20:23:00 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rrwob-00089J-97>; Mon, 30 Jan 2012 20:22:57 +0100 Received: from mail-we0-f182.google.com ([74.125.82.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rrwob-0006XQ-5C>; Mon, 30 Jan 2012 20:22:57 +0100 Received: by werm13 with SMTP id m13so3061805wer.13 for ; Mon, 30 Jan 2012 11:22:56 -0800 (PST) Received-SPF: pass (google.com: domain of mekentosj@gmail.com designates 10.180.77.200 as permitted sender) client-ip=10.180.77.200; Authentication-Results: mr.google.com; spf=pass (google.com: domain of mekentosj@gmail.com designates 10.180.77.200 as permitted sender) smtp.mail=mekentosj@gmail.com; dkim=pass header.i=mekentosj@gmail.com Received: from mr.google.com ([10.180.77.200]) by 10.180.77.200 with SMTP id u8mr35386561wiw.18.1327951376952 (num_hops = 1); Mon, 30 Jan 2012 11:22:56 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type:content-transfer-encoding; bh=uzs5qD8z9YdQE8mHomtFxpR1c4MJYFCFhijPayQLCtY=; b=GZY2s9rMdObBl1SeLhI94H9zaXxx/B07EQvxETxSf0MBxxFhhqj7FOqSG54DvBFy/5 N0w3KWBjinnMBeo+v7PJq1LDFyukcL+y+zJMEG8QkldPPUXhU2dzWSDfBzPeGKSO+Tid SiMuyl+E0Gq/WXXbQV1Jmkp2QqCtD/FRpiePM= MIME-Version: 1.0 Received: by 10.180.77.200 with SMTP id u8mr29539473wiw.18.1327951376875; Mon, 30 Jan 2012 11:22:56 -0800 (PST) Received: by 10.180.77.133 with HTTP; Mon, 30 Jan 2012 11:22:56 -0800 (PST) In-Reply-To: <286597EF-C118-4E12-947E-AAD31A024F5D@campus.fu-berlin.de> References: <286597EF-C118-4E12-947E-AAD31A024F5D@campus.fu-berlin.de> Date: Mon, 30 Jan 2012 19:22:56 +0000 Message-ID: From: Alexander Griekspoor To: SeqAn Development Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable X-Originating-IP: 74.125.82.182 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1327951377-000049E7-5734E450/3512801839-0/0-1 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: x X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, FU_XPURGATE_SUSP,RCVD_BY_IP,SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] Using seqan in stock Xcode project X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 30 Jan 2012 19:23:01 -0000 That would be great, thanks Dave. Alex On Mon, Jan 30, 2012 at 7:20 PM, Weese, David w= rote: > Ah, you are using the release version of Seqan. That would explain some i= ssues, as I had to rename some identifiers, e.g. id, before Seqan could be = used with Objective C. These diffs are not released yet so I suggest you to= use the svn trunk for now. The diffs are: > > http://trac.seqan.de/search?q=3Dobjective+c > > I can send you my xcode.app file tomorrow after it tested it under Lion. > > Dave > > Am 30.01.2012 um 20:04 schrieb Alexander Griekspoor: > >> Hi David, >> >> No, I have created a plain vanilla project using File -> New Project, >> then added the headers from the 1.3 release download. I wanted to >> avoid having to use CMake or the Xcode project it produces that >> contains all the 136 seqAn targets. I figured it should be one of the >> build settings. Would you or anyone have an example Xcode project that >> is setup in the way I described or an Xcode project that works for >> comparison purposes? >> Many thanks, >> Alex >> >> On Mon, Jan 30, 2012 at 6:25 PM, Weese, David wrote: >>> Hi Alex, >>> >>> I have no explanation for these errors. Have you created your Xcode pro= ject with CMake? This should compile flawlessly on OS X Lion with LLVM 3.0 = and also GCC 4.2. Maybe you do and compare the compilation fags of the two = project files. >>> >>> You can ignore the wiki page you have found. It describes how to use LL= VM 3.0 under Snow Leopard. >>> >>> Regards, >>> David >>> >>> Am 30.01.2012 um 00:48 schrieb Alexander Griekspoor: >>> >>>> To follow up on my last email, the warnings shown while building with >>>> the LLVM/GCC4.2 compiler setting. If I try with the LLVM3.0 option >>>> (which would be preferred I guess) I get the following errors: >>>> >>>> https://mekentosj-private.s3.amazonaws.com/seqan3.png >>>> https://mekentosj-private.s3.amazonaws.com/seqan4.png >>>> >>>> it seems to struggle over the same file/lines. >>>> >>>> I did see this article: >>>> >>>> http://trac.seqan.de/wiki/HowTo/UseLatestClangInXcode#HowTo:Usethelate= stLLVMClanginXcode >>>> >>>> but it seems outdates since Xcode moved to LLVM 3.0 with C++ support >>>> in the mean time. >>>> Hope you have a way to get things going. >>>> Alex >>>> >>>> On Sun, Jan 29, 2012 at 11:37 PM, Alexander Griekspoor >>>> wrote: >>>>> Hi everybody, >>>>> >>>>> We're currently evaluating whether to use seqan in one or more of our >>>>> projects, at first glance it looks awesome! >>>>> I'm trying to get it to work in a stock Cocoa application Xcode >>>>> project but am bumping into a number of errors being spit out. >>>>> I'd ideally like to use it in a 32/64bit universal app. >>>>> >>>>> Two screenshots: >>>>> https://mekentosj-private.s3.amazonaws.com/seqan1.png >>>>> https://mekentosj-private.s3.amazonaws.com/seqan2.png >>>>> >>>>> And the simple test app: >>>>> https://mekentosj-private.s3.amazonaws.com/SeqanTest.zip >>>>> >>>>> Any clues how to set this up? >>>>> Many thanks! >>>>> Alex >>>>> >>>>> >>>>> >>>>> -- >>>>> **************************************************** >>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0** Alexander Griekspoor =C2=A0PhD *= * >>>>> **************************************************** >>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekent= osj.com >>>>> >>>>> =C2=A0Papers - Your Personal Library of Science >>>>> =C2=A0 =C2=A0 =C2=A0Winner of the Apple Design Awards >>>>> =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution >>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers >>>>> >>>>> =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers >>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0available wherever you go: >>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers/ipad >>>>> **************************************************** >>>> >>>> >>>> >>>> -- >>>> **************************************************** >>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0** Alexander Griekspoor =C2=A0PhD ** >>>> **************************************************** >>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekento= sj.com >>>> >>>> =C2=A0Papers - Your Personal Library of Science >>>> =C2=A0 =C2=A0 =C2=A0Winner of the Apple Design Awards >>>> =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution >>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers >>>> >>>> =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers >>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0available wherever you go: >>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers/ipad >>>> **************************************************** >>>> >>>> _______________________________________________ >>>> seqan-dev mailing list >>>> seqan-dev@lists.fu-berlin.de >>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>> >>> >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev >> >> >> >> -- >> **************************************************** >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0** Alexander Griekspoor =C2=A0PhD ** >> **************************************************** >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj= .com >> >> =C2=A0Papers - Your Personal Library of Science >> =C2=A0 =C2=A0 =C2=A0Winner of the Apple Design Awards >> =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers >> >> =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers >> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0available wherever you go: >> =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers/ipad >> **************************************************** >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev --=20 **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 ** Alexander Griekspoor=C2=A0 PhD ** **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj.co= m =C2=A0Papers - Your Personal Library of Science =C2=A0 =C2=A0=C2=A0 Winner of the Apple Design Awards =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 available wherever you go: =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers/ipad **************************************************** From mekentosj@gmail.com Mon Jan 30 23:41:39 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rrzuq-0005f1-Oi>; Mon, 30 Jan 2012 23:41:36 +0100 Received: from mail-wi0-f182.google.com ([209.85.212.182]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rrzuq-0000FL-KY>; Mon, 30 Jan 2012 23:41:36 +0100 Received: by wibhn14 with SMTP id hn14so5702620wib.13 for ; Mon, 30 Jan 2012 14:41:36 -0800 (PST) Received-SPF: pass (google.com: domain of mekentosj@gmail.com designates 10.180.95.105 as permitted sender) client-ip=10.180.95.105; Authentication-Results: mr.google.com; spf=pass (google.com: domain of mekentosj@gmail.com designates 10.180.95.105 as permitted sender) smtp.mail=mekentosj@gmail.com; dkim=pass header.i=mekentosj@gmail.com Received: from mr.google.com ([10.180.95.105]) by 10.180.95.105 with SMTP id dj9mr36309612wib.18.1327963296409 (num_hops = 1); Mon, 30 Jan 2012 14:41:36 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=gamma; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type:content-transfer-encoding; bh=fxVew25BKpvlUyS4n0OXcSNQjxnbX76LwbV9IDPDsdg=; b=bSBCDbanp3dODQ5YamtX3oWNi7KwrBbT4kW5RLv8DLr6CplYmClLKwNe0JWPoRdgwS UZw+Wj1Y4t7wBiOXBVqVYIT/x1Nab4+EFDsHKwiiuNiP88JE59ID0U0+F7eMebiI/z5H nxSDdJzIWde11ZgvcRe2JWMjgz0QgyAtT1UgY= MIME-Version: 1.0 Received: by 10.180.95.105 with SMTP id dj9mr30273692wib.18.1327963296305; Mon, 30 Jan 2012 14:41:36 -0800 (PST) Received: by 10.180.77.133 with HTTP; Mon, 30 Jan 2012 14:41:35 -0800 (PST) In-Reply-To: References: <286597EF-C118-4E12-947E-AAD31A024F5D@campus.fu-berlin.de> Date: Mon, 30 Jan 2012 22:41:35 +0000 Message-ID: From: Alexander Griekspoor To: SeqAn Development Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable X-Originating-IP: 209.85.212.182 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327963296-000049E7-B02F99BF/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, RCVD_BY_IP, SPF_HELO_PASS,SPF_PASS Subject: Re: [Seqan-dev] Using seqan in stock Xcode project X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 30 Jan 2012 22:41:39 -0000 Hi Dave, Good news, I managed to get things to compile with help of your instructions, thank you so much! For future reference here's what I did (pretty much as Dave suggested): - create a stock Cocoa app in Xcode4 using File -> New Project (using ARC) - renamed AppDelegate.m to AppDelegate.mm, import seqan.h - followed the steps Dave outlined to get all forwards: cd seqan-trunk mkdir build; cd build cmake .. -G "Unix Makefiles" make alignment - did one extra make to get the the forwards for build/extras/include that make alignment doesn't create: make alf - in the Xcode build settings added the following User header paths: seqan-trunk/core/include seqan-trunk/extras/include seqan-trunk/build/core/include seqan-trunk/build/extras/include - and activate the Always Search User Paths option to YES that's it. I do get about 100 of these warnings: /Users/mekentosj/molbio/seqan-trunk/core/include/seqan/random/random_mt1993= 7.h:90:16:{90:16-90:33}{90:9-90:15}: warning: implicit conversion loses integer precision: 'MTRand::uint32' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32,3] not sure how we could avoid these? Again, many thanks for the help, the library looks very promising and we're seriously considering using it in one or more future products. To be continued=E2=80=A6 Alex On Mon, Jan 30, 2012 at 7:22 PM, Alexander Griekspoor wrote: > That would be great, thanks Dave. > Alex > > On Mon, Jan 30, 2012 at 7:20 PM, Weese, David = wrote: >> Ah, you are using the release version of Seqan. That would explain some = issues, as I had to rename some identifiers, e.g. id, before Seqan could be= used with Objective C. These diffs are not released yet so I suggest you t= o use the svn trunk for now. The diffs are: >> >> http://trac.seqan.de/search?q=3Dobjective+c >> >> I can send you my xcode.app file tomorrow after it tested it under Lion. >> >> Dave >> >> Am 30.01.2012 um 20:04 schrieb Alexander Griekspoor: >> >>> Hi David, >>> >>> No, I have created a plain vanilla project using File -> New Project, >>> then added the headers from the 1.3 release download. I wanted to >>> avoid having to use CMake or the Xcode project it produces that >>> contains all the 136 seqAn targets. I figured it should be one of the >>> build settings. Would you or anyone have an example Xcode project that >>> is setup in the way I described or an Xcode project that works for >>> comparison purposes? >>> Many thanks, >>> Alex >>> >>> On Mon, Jan 30, 2012 at 6:25 PM, Weese, David wrote: >>>> Hi Alex, >>>> >>>> I have no explanation for these errors. Have you created your Xcode pr= oject with CMake? This should compile flawlessly on OS X Lion with LLVM 3.0= and also GCC 4.2. Maybe you do and compare the compilation fags of the two= project files. >>>> >>>> You can ignore the wiki page you have found. It describes how to use L= LVM 3.0 under Snow Leopard. >>>> >>>> Regards, >>>> David >>>> >>>> Am 30.01.2012 um 00:48 schrieb Alexander Griekspoor: >>>> >>>>> To follow up on my last email, the warnings shown while building with >>>>> the LLVM/GCC4.2 compiler setting. If I try with the LLVM3.0 option >>>>> (which would be preferred I guess) I get the following errors: >>>>> >>>>> https://mekentosj-private.s3.amazonaws.com/seqan3.png >>>>> https://mekentosj-private.s3.amazonaws.com/seqan4.png >>>>> >>>>> it seems to struggle over the same file/lines. >>>>> >>>>> I did see this article: >>>>> >>>>> http://trac.seqan.de/wiki/HowTo/UseLatestClangInXcode#HowTo:Usethelat= estLLVMClanginXcode >>>>> >>>>> but it seems outdates since Xcode moved to LLVM 3.0 with C++ support >>>>> in the mean time. >>>>> Hope you have a way to get things going. >>>>> Alex >>>>> >>>>> On Sun, Jan 29, 2012 at 11:37 PM, Alexander Griekspoor >>>>> wrote: >>>>>> Hi everybody, >>>>>> >>>>>> We're currently evaluating whether to use seqan in one or more of ou= r >>>>>> projects, at first glance it looks awesome! >>>>>> I'm trying to get it to work in a stock Cocoa application Xcode >>>>>> project but am bumping into a number of errors being spit out. >>>>>> I'd ideally like to use it in a 32/64bit universal app. >>>>>> >>>>>> Two screenshots: >>>>>> https://mekentosj-private.s3.amazonaws.com/seqan1.png >>>>>> https://mekentosj-private.s3.amazonaws.com/seqan2.png >>>>>> >>>>>> And the simple test app: >>>>>> https://mekentosj-private.s3.amazonaws.com/SeqanTest.zip >>>>>> >>>>>> Any clues how to set this up? >>>>>> Many thanks! >>>>>> Alex >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> **************************************************** >>>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0** Alexander Griekspoor =C2=A0PhD = ** >>>>>> **************************************************** >>>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 meken= tosj.com >>>>>> >>>>>> =C2=A0Papers - Your Personal Library of Science >>>>>> =C2=A0 =C2=A0 =C2=A0Winner of the Apple Design Awards >>>>>> =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution >>>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers >>>>>> >>>>>> =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers >>>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0available wherever you go: >>>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers/ipad >>>>>> **************************************************** >>>>> >>>>> >>>>> >>>>> -- >>>>> **************************************************** >>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0** Alexander Griekspoor =C2=A0PhD *= * >>>>> **************************************************** >>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekent= osj.com >>>>> >>>>> =C2=A0Papers - Your Personal Library of Science >>>>> =C2=A0 =C2=A0 =C2=A0Winner of the Apple Design Awards >>>>> =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution >>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers >>>>> >>>>> =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers >>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0available wherever you go: >>>>> =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers/ipad >>>>> **************************************************** >>>>> >>>>> _______________________________________________ >>>>> seqan-dev mailing list >>>>> seqan-dev@lists.fu-berlin.de >>>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>> >>>> >>>> _______________________________________________ >>>> seqan-dev mailing list >>>> seqan-dev@lists.fu-berlin.de >>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>> >>> >>> >>> -- >>> **************************************************** >>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0** Alexander Griekspoor =C2=A0PhD ** >>> **************************************************** >>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentos= j.com >>> >>> =C2=A0Papers - Your Personal Library of Science >>> =C2=A0 =C2=A0 =C2=A0Winner of the Apple Design Awards >>> =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution >>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers >>> >>> =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers >>> =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0available wherever you go: >>> =C2=A0 =C2=A0 =C2=A0 =C2=A0http://mekentosj.com/papers/ipad >>> **************************************************** >>> >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev >> >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev > > > > -- > **************************************************** > =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 ** Alexander Griekspoor=C2=A0 PhD ** > **************************************************** > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj.= com > > =C2=A0Papers - Your Personal Library of Science > =C2=A0 =C2=A0=C2=A0 Winner of the Apple Design Awards > =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution > =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers > > =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 available wherever you go: > =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers/ipad > **************************************************** --=20 **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 ** Alexander Griekspoor=C2=A0 PhD ** **************************************************** =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 mekentosj.co= m =C2=A0Papers - Your Personal Library of Science =C2=A0 =C2=A0=C2=A0 Winner of the Apple Design Awards =C2=A0 =C2=A0 =C2=A0 Best Mac OS X Scientific Solution =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers =C2=A0 =C2=A0 =C2=A0Papers for iPad - all your papers =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 available wherever you go: =C2=A0 =C2=A0 =C2=A0=C2=A0 http://mekentosj.com/papers/ipad **************************************************** From weese@campus.fu-berlin.de Tue Jan 31 09:40:14 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rs9G7-0007Fu-SY>; Tue, 31 Jan 2012 09:40:12 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rs9G7-0004gQ-QT>; Tue, 31 Jan 2012 09:40:11 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Rs9G7-0004XF-Kv>; Tue, 31 Jan 2012 09:40:11 +0100 Received: from exchange6.fu-berlin.de ([160.45.9.133]) by exchange6.fu-berlin.de ([160.45.9.133]) with mapi; Tue, 31 Jan 2012 09:40:11 +0100 From: "Weese, David" To: SeqAn Development Date: Tue, 31 Jan 2012 09:40:10 +0100 Thread-Topic: [Seqan-dev] Using seqan in stock Xcode project Thread-Index: Aczf8/GSFCIBIShfQ1+HOeOx3Dfb8Q== Message-ID: References: <286597EF-C118-4E12-947E-AAD31A024F5D@campus.fu-berlin.de> In-Reply-To: Accept-Language: de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: de-DE Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Originating-IP: 160.45.9.133 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1327999211-000049E7-85D3CF0E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Checker-Version: SpamAssassin 3.0.4 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED Subject: Re: [Seqan-dev] Using seqan in stock Xcode project X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.11 Precedence: list Reply-To: SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 31 Jan 2012 08:40:14 -0000 Hi Alex, that' sounds good and you're welcome. We'll have a look at the conversion w= arning. For now you could try changing: typedef unsigned long uint32; into typedef unsigned uint32; in line 76 of seqan/core/include/seqan/random/ext_MersenneTwister.h Cheers, Dave David Weese weese@inf.fu-berlin.de Freie Universit=E4t Berlin http://www.inf.fu-berlin.de/ Institut f=FCr Informatik Phone: +49 30 838 75246 Takustra=DFe 9 Algorithmic Bioinformatics 14195 Berlin Room 021=20 Am 30.01.2012 um 23:41 schrieb Alexander Griekspoor: > Hi Dave, >=20 > Good news, I managed to get things to compile with help of your > instructions, thank you so much! > For future reference here's what I did (pretty much as Dave suggested): >=20 > - create a stock Cocoa app in Xcode4 using File -> New Project (using AR= C) > - renamed AppDelegate.m to AppDelegate.mm, import seqan.h > - followed the steps Dave outlined to get all forwards: >=20 > cd seqan-trunk > mkdir build; cd build > cmake .. -G "Unix Makefiles" > make alignment >=20 > - did one extra make to get the the forwards for build/extras/include > that make alignment doesn't create: >=20 > make alf >=20 > - in the Xcode build settings added the following User header paths: >=20 > seqan-trunk/core/include > seqan-trunk/extras/include > seqan-trunk/build/core/include > seqan-trunk/build/extras/include >=20 > - and activate the Always Search User Paths option to YES >=20 > that's it. >=20 > I do get about 100 of these warnings: >=20 > /Users/mekentosj/molbio/seqan-trunk/core/include/seqan/random/random_mt19= 937.h:90:16:{90:16-90:33}{90:9-90:15}: > warning: implicit conversion loses integer precision: 'MTRand::uint32' > (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32,3] >=20 > not sure how we could avoid these? >=20 > Again, many thanks for the help, the library looks very promising and > we're seriously considering using it in one or more future products. > To be continued=85 > Alex >=20 >=20 >=20 > On Mon, Jan 30, 2012 at 7:22 PM, Alexander Griekspoor > wrote: >> That would be great, thanks Dave. >> Alex >>=20 >> On Mon, Jan 30, 2012 at 7:20 PM, Weese, David wrote: >>> Ah, you are using the release version of Seqan. That would explain some= issues, as I had to rename some identifiers, e.g. id, before Seqan could b= e used with Objective C. These diffs are not released yet so I suggest you = to use the svn trunk for now. The diffs are: >>>=20 >>> http://trac.seqan.de/search?q=3Dobjective+c >>>=20 >>> I can send you my xcode.app file tomorrow after it tested it under Lion= . >>>=20 >>> Dave >>>=20 >>> Am 30.01.2012 um 20:04 schrieb Alexander Griekspoor: >>>=20 >>>> Hi David, >>>>=20 >>>> No, I have created a plain vanilla project using File -> New Project, >>>> then added the headers from the 1.3 release download. I wanted to >>>> avoid having to use CMake or the Xcode project it produces that >>>> contains all the 136 seqAn targets. I figured it should be one of the >>>> build settings. Would you or anyone have an example Xcode project that >>>> is setup in the way I described or an Xcode project that works for >>>> comparison purposes? >>>> Many thanks, >>>> Alex >>>>=20 >>>> On Mon, Jan 30, 2012 at 6:25 PM, Weese, David wrote: >>>>> Hi Alex, >>>>>=20 >>>>> I have no explanation for these errors. Have you created your Xcode p= roject with CMake? This should compile flawlessly on OS X Lion with LLVM 3.= 0 and also GCC 4.2. Maybe you do and compare the compilation fags of the tw= o project files. >>>>>=20 >>>>> You can ignore the wiki page you have found. It describes how to use = LLVM 3.0 under Snow Leopard. >>>>>=20 >>>>> Regards, >>>>> David >>>>>=20 >>>>> Am 30.01.2012 um 00:48 schrieb Alexander Griekspoor: >>>>>=20 >>>>>> To follow up on my last email, the warnings shown while building wit= h >>>>>> the LLVM/GCC4.2 compiler setting. If I try with the LLVM3.0 option >>>>>> (which would be preferred I guess) I get the following errors: >>>>>>=20 >>>>>> https://mekentosj-private.s3.amazonaws.com/seqan3.png >>>>>> https://mekentosj-private.s3.amazonaws.com/seqan4.png >>>>>>=20 >>>>>> it seems to struggle over the same file/lines. >>>>>>=20 >>>>>> I did see this article: >>>>>>=20 >>>>>> http://trac.seqan.de/wiki/HowTo/UseLatestClangInXcode#HowTo:Usethela= testLLVMClanginXcode >>>>>>=20 >>>>>> but it seems outdates since Xcode moved to LLVM 3.0 with C++ support >>>>>> in the mean time. >>>>>> Hope you have a way to get things going. >>>>>> Alex >>>>>>=20 >>>>>> On Sun, Jan 29, 2012 at 11:37 PM, Alexander Griekspoor >>>>>> wrote: >>>>>>> Hi everybody, >>>>>>>=20 >>>>>>> We're currently evaluating whether to use seqan in one or more of o= ur >>>>>>> projects, at first glance it looks awesome! >>>>>>> I'm trying to get it to work in a stock Cocoa application Xcode >>>>>>> project but am bumping into a number of errors being spit out. >>>>>>> I'd ideally like to use it in a 32/64bit universal app. >>>>>>>=20 >>>>>>> Two screenshots: >>>>>>> https://mekentosj-private.s3.amazonaws.com/seqan1.png >>>>>>> https://mekentosj-private.s3.amazonaws.com/seqan2.png >>>>>>>=20 >>>>>>> And the simple test app: >>>>>>> https://mekentosj-private.s3.amazonaws.com/SeqanTest.zip >>>>>>>=20 >>>>>>> Any clues how to set this up? >>>>>>> Many thanks! >>>>>>> Alex >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>> -- >>>>>>> **************************************************** >>>>>>> ** Alexander Griekspoor PhD ** >>>>>>> **************************************************** >>>>>>> mekentosj.com >>>>>>>=20 >>>>>>> Papers - Your Personal Library of Science >>>>>>> Winner of the Apple Design Awards >>>>>>> Best Mac OS X Scientific Solution >>>>>>> http://mekentosj.com/papers >>>>>>>=20 >>>>>>> Papers for iPad - all your papers >>>>>>> available wherever you go: >>>>>>> http://mekentosj.com/papers/ipad >>>>>>> **************************************************** >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>> -- >>>>>> **************************************************** >>>>>> ** Alexander Griekspoor PhD ** >>>>>> **************************************************** >>>>>> mekentosj.com >>>>>>=20 >>>>>> Papers - Your Personal Library of Science >>>>>> Winner of the Apple Design Awards >>>>>> Best Mac OS X Scientific Solution >>>>>> http://mekentosj.com/papers >>>>>>=20 >>>>>> Papers for iPad - all your papers >>>>>> available wherever you go: >>>>>> http://mekentosj.com/papers/ipad >>>>>> **************************************************** >>>>>>=20 >>>>>> _______________________________________________ >>>>>> seqan-dev mailing list >>>>>> seqan-dev@lists.fu-berlin.de >>>>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>>>=20 >>>>>=20 >>>>> _______________________________________________ >>>>> seqan-dev mailing list >>>>> seqan-dev@lists.fu-berlin.de >>>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>>=20 >>>>=20 >>>>=20 >>>> -- >>>> **************************************************** >>>> ** Alexander Griekspoor PhD ** >>>> **************************************************** >>>> mekentosj.com >>>>=20 >>>> Papers - Your Personal Library of Science >>>> Winner of the Apple Design Awards >>>> Best Mac OS X Scientific Solution >>>> http://mekentosj.com/papers >>>>=20 >>>> Papers for iPad - all your papers >>>> available wherever you go: >>>> http://mekentosj.com/papers/ipad >>>> **************************************************** >>>>=20 >>>> _______________________________________________ >>>> seqan-dev mailing list >>>> seqan-dev@lists.fu-berlin.de >>>> https://lists.fu-berlin.de/listinfo/seqan-dev >>>=20 >>>=20 >>> _______________________________________________ >>> seqan-dev mailing list >>> seqan-dev@lists.fu-berlin.de >>> https://lists.fu-berlin.de/listinfo/seqan-dev >>=20 >>=20 >>=20 >> -- >> **************************************************** >> ** Alexander Griekspoor PhD ** >> **************************************************** >> mekentosj.com >>=20 >> Papers - Your Personal Library of Science >> Winner of the Apple Design Awards >> Best Mac OS X Scientific Solution >> http://mekentosj.com/papers >>=20 >> Papers for iPad - all your papers >> available wherever you go: >> http://mekentosj.com/papers/ipad >> **************************************************** >=20 >=20 >=20 > -- > **************************************************** > ** Alexander Griekspoor PhD ** > **************************************************** > mekentosj.com >=20 > Papers - Your Personal Library of Science > Winner of the Apple Design Awards > Best Mac OS X Scientific Solution > http://mekentosj.com/papers >=20 > Papers for iPad - all your papers > available wherever you go: > http://mekentosj.com/papers/ipad > **************************************************** >=20 > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev