I'm trying to build a tool with=C2=A0S= eqAn=C2= =A0to quickly align some PacBio data, using "bandedChainAlignment"= ;, but I'm consistently getting a crash during the trace-back step.=C2= =A0 The generation of the Seeds (SuffixArray) and the finding of the base S= eedChain works fine, but the final step of turning that into an alignment d= oesn't appear to work. =C2=A0

Suggestions?

Error Log:

&quo= t;""

bbowman@localhost:~/git/SRSLI$ ./src/C++/srsl= i test/data/query/ecoli_5p_sample.fastq test/data/reference/ecoliK12_5p_ass= embly.fasta=C2=A0

Query 0

Finished finding seeds

<= div>Finishing chaining seeds

Starting alignment of sequences

/usr/include/s= eqan/seeds/banded_chain_alignment_traceback.h:195 Assertion failed := isGlued =3D=3D true was: 0 !=3D 1 (Fatal error while trying to connect tra= ce backs: No glue point available!)

Aborted (core dumped)

"""

-Brett

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b=yzlz4sjhPEumNRFiNxJRnfQ57NdbbBSNOgj9F18pmL/rHlmCe+aLnG7t2p6kufV8np AT2jS3N0KQEucyZKzbgfO2ySkaKKxfbV3iQV1kvCp+SywjwebsnWF5PWhaLBc6qqNGMt S6x2xKCx9bRriBlAH9xz9h7HPN6SCVda0VDQypAcnUXqAx10kQOjhGGHfq5IcqUIRAtn cYa3HLNKSbxJSFSzCnDuruV6QkceCZLwvXMKr+E2kMEv7w9J52f10rwaXzNzqOyVjFFY lCQ68lLI5LZWeYo4UDNqr/STMBcRC/KAQQIa+TEWjvEEBTI45241G+IqMIEnGPuADU7W YXaQ== X-Received: by 10.180.21.210 with SMTP id x18mr26027989wie.19.1416172485273; Sun, 16 Nov 2014 13:14:45 -0800 (PST) Received: from localhost.localdomain ([46.227.4.49]) by mx.google.com with ESMTPSA id cu9sm48885491wjb.0.2014.11.16.13.14.43 for (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Sun, 16 Nov 2014 13:14:44 -0800 (PST) Message-ID: <546913C0.3060606@gmail.com> Date: Sun, 16 Nov 2014 22:14:40 +0100 From: Antonio Trande User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:31.0) Gecko/20100101 Thunderbird/31.2.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit X-Originating-IP: 74.125.82.48 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416172486-00067E64-6A8E080D/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.016304, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] [seqan-1.4.2] breakpoint_calculator errors X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 16 Nov 2014 21:14:48 -0000 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all. I need your help with these errors during SeqAn compilation on Fedora 21. Here the full log: https://kojipkgs.fedoraproject.org//work/tasks/2027/8162027/build.log - -- Antonio Trande mailto: sagitter 'at' fedoraproject 'dot' org http://fedoraos.wordpress.com/ https://fedoraproject.org/wiki/User:Sagitter GPG Key: 0x66E15D00 Check on https://keys.fedoraproject.org/ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBAgAGBQJUaRPAAAoJEFyovWBm4V0A3+cQAJJQgQuBXdj9hsH0PKcuZ+r3 EyrZK0OoUdVJvtF1TUUpDPnJHVL1ZbvJN0ks4C2hGT0McMMKTy+zXHdIYlGqliXW Lxhl0pJFTQwFj2p7xnbY7D+31vBOfCLqaClId9ZLwij7sUu0zYsD8d7up99JkmrE TmblYcJmE8lechG6dmz7tW25gobcdY+Y7M7e435aCrLDHrntkE3H1YtXJOB5l11y 4otH4hd0Vo4bap//NvOZKtDSoyC46WS2ZAEOKghNwzOjdETDbubWsdsDwqK5Td98 DUfFTjCFk/AoGLxeoBCGzpVDDqr5zrbXCAaOvXwbXp8D97c3tYCnjqII9l/i570k oYdJTCmvZFbx5YkG+u2pLq5DBmtC0ikQC+/f0bBlwAsoEoN8OymcIIyw+fjPLJ4t gMXzqJcKCci5pAqevKDrz49lvAfeWLg52Ud7eQUpwe6eWcDA08gvggphboAzsiMS GNkxEhvQKW1Tk5KkuRLz+VeuNOC8JNPRNDHiKNHA76wdtb+NJPQlvr2/3Qz87g+i zIkO4Svz/pzltc/RUwIQaDQxRe5Cadfnv5NWKOWA5iZ3xYBJqU8t7+um79XyY4sb 3NoZ9z/vBkmm8J5FOtsLusdWzGo0UcX0j1OAmd6mqmh//bJZ1Bb0WhgTjgERMr83 VOKNsl2dzVuYbvofCIQs =ngAX -----END PGP SIGNATURE----- From bnbowman@gmail.com Mon Nov 17 06:39:48 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XqF2Q-00356a-5W>; Mon, 17 Nov 2014 06:39:46 +0100 Received: from mail-yk0-f169.google.com ([209.85.160.169]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XqF2P-000XtX-Ne>; Mon, 17 Nov 2014 06:39:46 +0100 Received: by mail-yk0-f169.google.com with SMTP id 79so2050633ykr.14 for ; Sun, 16 Nov 2014 21:39:42 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=8jHIWa1PDeSRODZA8eTIQdE9fs+iszpovTNtKMjZZ1E=; b=TIfP5pjcX1VRLbz7wewTrPOpNvsimsG+ffdyX7BnpZ+N6/ufDrIl/3OL/BxCI22DsY PpT05zFtyya/3OqS0ecit053EY9qU3GT4iwEkNNg0ij1JJhuJelCOOd/4jL7DbcvfIcG pC/KY14LEuhzuMr1sEc2MjQcJwybvx3klu87JqJ/RSzw9qTTJJrvJGamSjOrroUjFmCu XA98UbiIqRpouZpGYqA4XFhxZfHz2VYhJ4RJCpaeo+Jk1miQWThnm1CZVR8uAEeJ1ucR /ZpCp4LG+zp6BIXhYjVAQWzN5H+2jR4w25Qr58lEWxT/0Moxt93VuuO/+oFLqzO47ujR ENQQ== MIME-Version: 1.0 X-Received: by 10.236.199.3 with SMTP id w3mr23280394yhn.20.1416202781809; Sun, 16 Nov 2014 21:39:41 -0800 (PST) Received: by 10.170.110.19 with HTTP; Sun, 16 Nov 2014 21:39:41 -0800 (PST) In-Reply-To: <50D46377-BAED-47B3-8091-6DF539B7C9E8@fritz.box> References: <50D46377-BAED-47B3-8091-6DF539B7C9E8@fritz.box> Date: Sun, 16 Nov 2014 21:39:41 -0800 Message-ID: From: Brett Bowman To: SeqAn Development Content-Type: multipart/mixed; boundary=089e0160b074bd7b600508076746 X-Originating-IP: 209.85.160.169 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416202786-00067E64-6C2CC6E6/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.426887, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Fatal Error in Banded Chain Alignment Traceback X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 17 Nov 2014 05:39:48 -0000 --089e0160b074bd7b600508076746 Content-Type: multipart/alternative; boundary=089e0160b074bd7b540508076744 --089e0160b074bd7b540508076744 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks Rene, My query, reference, and canonical alignment from BLASR (the PacBio-specific aligner) attached. I also noticed that the seeds it's chaining with chainGlobalAlignment() are way off the diagonal, which may be related - details below: """ Query #1 - m130404_014004_sidney_c100506902550000001823076808221337_s1_p0/5779/0_10397 Finished finding seeds Seeds: 1939 Finishing chaining seeds Chain: 44 Seed(7688, 57, 7706, 75, lower diag =3D 7631, upper diag = =3D 7631) Length: 18 Seed(7707, 94, 7722, 109, lower diag =3D 7613, upper diag = =3D 7613) Length: 15 Seed(7933, 111, 7946, 124, lower diag =3D 7822, upper diag= =3D 7822) Length: 13 Seed(7949, 130, 7965, 146, lower diag =3D 7819, upper diag= =3D 7819) Length: 16 Seed(8065, 299, 8078, 312, lower diag =3D 7766, upper diag= =3D 7766) Length: 13 Seed(8109, 314, 8126, 331, lower diag =3D 7795, upper diag= =3D 7795) Length: 17 Seed(8169, 363, 8181, 375, lower diag =3D 7806, upper diag= =3D 7806) Length: 12 Seed(8208, 381, 8222, 395, lower diag =3D 7827, upper diag= =3D 7827) Length: 14 Seed(8222, 402, 8234, 414, lower diag =3D 7820, upper diag= =3D 7820) Length: 12 Seed(8287, 446, 8304, 463, lower diag =3D 7841, upper diag= =3D 7841) Length: 17 Seed(8304, 466, 8316, 478, lower diag =3D 7838, upper diag= =3D 7838) Length: 12 Seed(8326, 748, 8338, 760, lower diag =3D 7578, upper diag= =3D 7578) Length: 12 Seed(8354, 761, 8366, 773, lower diag =3D 7593, upper diag= =3D 7593) Length: 12 Seed(8426, 801, 8438, 813, lower diag =3D 7625, upper diag= =3D 7625) Length: 12 Seed(8702, 2291, 8721, 2310, lower diag =3D 6411, upper di= ag =3D 6411) Length: 19 Seed(8769, 2314, 8781, 2326, lower diag =3D 6455, upper di= ag =3D 6455) Length: 12 Seed(8794, 2387, 8806, 2399, lower diag =3D 6407, upper di= ag =3D 6407) Length: 12 Seed(8835, 2400, 8847, 2412, lower diag =3D 6435, upper di= ag =3D 6435) Length: 12 Seed(9162, 2650, 9174, 2662, lower diag =3D 6512, upper di= ag =3D 6512) Length: 12 Seed(9184, 2676, 9196, 2688, lower diag =3D 6508, upper di= ag =3D 6508) Length: 12 Seed(9196, 2736, 9208, 2748, lower diag =3D 6460, upper di= ag =3D 6460) Length: 12 Seed(9223, 2818, 9235, 2830, lower diag =3D 6405, upper di= ag =3D 6405) Length: 12 Seed(9251, 2844, 9267, 2860, lower diag =3D 6407, upper di= ag =3D 6407) Length: 16 Seed(9294, 2871, 9308, 2885, lower diag =3D 6423, upper di= ag =3D 6423) Length: 14 Seed(9314, 2891, 9327, 2904, lower diag =3D 6423, upper di= ag =3D 6423) Length: 13 Seed(9432, 2976, 9447, 2991, lower diag =3D 6456, upper di= ag =3D 6456) Length: 15 Seed(9515, 2992, 9527, 3004, lower diag =3D 6523, upper di= ag =3D 6523) Length: 12 Seed(9675, 3385, 9701, 3411, lower diag =3D 6290, upper di= ag =3D 6290) Length: 26 Seed(9724, 3414, 9736, 3426, lower diag =3D 6310, upper di= ag =3D 6310) Length: 12 Seed(9791, 3571, 9804, 3584, lower diag =3D 6220, upper di= ag =3D 6220) Length: 13 Seed(9805, 3596, 9817, 3608, lower diag =3D 6209, upper di= ag =3D 6209) Length: 12 Seed(9818, 4915, 9830, 4927, lower diag =3D 4903, upper di= ag =3D 4903) Length: 12 Seed(9842, 4939, 9854, 4951, lower diag =3D 4903, upper di= ag =3D 4903) Length: 12 Seed(9873, 5045, 9885, 5057, lower diag =3D 4828, upper di= ag =3D 4828) Length: 12 Seed(9886, 5077, 9898, 5089, lower diag =3D 4809, upper di= ag =3D 4809) Length: 12 Seed(9943, 5242, 9955, 5254, lower diag =3D 4701, upper di= ag =3D 4701) Length: 12 Seed(9957, 5385, 9969, 5397, lower diag =3D 4572, upper di= ag =3D 4572) Length: 12 Seed(9994, 5423, 10006, 5435, lower diag =3D 4571, upper diag =3D 4571) Length: 12 Seed(10062, 7096, 10074, 7108, lower diag =3D 2966, upper diag =3D 2966) Length: 12 Seed(10102, 7109, 10114, 7121, lower diag =3D 2993, upper diag =3D 2993) Length: 12 Seed(10156, 7131, 10178, 7153, lower diag =3D 3025, upper diag =3D 3025) Length: 22 Seed(10277, 7354, 10299, 7376, lower diag =3D 2923, upper diag =3D 2923) Length: 22 Seed(10299, 7378, 10313, 7392, lower diag =3D 2921, upper diag =3D 2921) Length: 14 Seed(10371, 7400, 10385, 7414, lower diag =3D 2971, upper diag =3D 2971) Length: 14 """ -Brett On Sun, Nov 16, 2014 at 2:57 AM, Rahn, Ren=C3=A9 wrote: > Hey Brett, > > It could have multiple reasons. > In general, it means that there was a traceback path from a seed or a gap= , > that couldn=E2=80=99t be connected with one of the so far generated trace= back > paths. Note, that the traceback is computed incrementally to reduce the > space requirements. > If you could send me a simple text file containing the seeds of the seed > chain (one seed per row using the <<-operator), that is input to the band= ed > chain alignment function, I could have a look at it and fix the problem. > Also, I opened an issue in github: > https://github.com/seqan/seqan/issues/699, for tracking the issue. > > > Kind regards, > > Ren=C3=A9 Rahn > > On 16 Nov 2014, at 04:17, Brett Bowman wrote: > > I'm trying to build a tool with SeqAn to quickly align some PacBio data, > using "bandedChainAlignment", but I'm consistently getting a crash during > the trace-back step. The generation of the Seeds (SuffixArray) and the > finding of the base SeedChain works fine, but the final step of turning > that into an alignment doesn't appear to work. > > Suggestions? > > Error Log: > """ > bbowman@localhost:~/git/SRSLI$ ./src/C++/srsli > test/data/query/ecoli_5p_sample.fastq > test/data/reference/ecoliK12_5p_assembly.fasta > Query 0 > Finished finding seeds > Finishing chaining seeds > Starting alignment of sequences > /usr/include/seqan/seeds/banded_chain_alignment_traceback.h:195 Assertion > failed : isGlued =3D=3D true was: 0 !=3D 1 (Fatal error while trying to c= onnect > trace backs: No glue point available!) > Aborted (core dumped) > """ > > -Brett > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > > --- > > Ren=C3=A9 Rahn > Ph.D. Student > -------------------------------- > Tel: (+49) 30 838 75277 > Mail: rene.rahn@fu-berlin.de > -------------------------------- > Institute of Computer Science > Algorithmic Bioinformatics (ABI) > -------------------------------- > Freie Universit=C3=A4t Berlin > Takustra=C3=9Fe 9 > 14195 Berlin > -------------------------------- > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > --089e0160b074bd7b540508076744 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Thanks Rene,

My query, reference,= and canonical alignment from BLASR (the PacBio-specific aligner) attached.=

I also noticed that the seeds it's chaining with ch= ainGlobalAlignment() are way off the diagonal, which may be related - detai= ls below:=C2=A0

"""

Qu= ery #1 - m130404_014004_sidney_c100506902550000001823076808221337_s1_p0/577= 9/0_10397

Finished finding seeds

Seeds: 1939

= Finishing chaining seeds

Chain: 44

Seed<Simple, TCon= fig>(7688, 57, 7706, 75, lower diag =3D 7631, upper diag =3D 7631) Lengt= h: 18

Seed<Simple, TConfig>(7707, 94, 7722, 109, lower diag= =3D 7613, upper diag =3D 7613) Length: 15

Seed<Simple, TConfi= g>(7933, 111, 7946, 124, lower diag =3D 7822, upper diag =3D 7822) Lengt= h: 13

Seed<Simple, TConfig>(7949, 130, 7965, 146, lower dia= g =3D 7819, upper diag =3D 7819) Length: 16

Seed<Simple, TConf= ig>(8065, 299, 8078, 312, lower diag =3D 7766, upper diag =3D 7766) Leng= th: 13

Seed<Simple, TConfig>(8109, 314, 8126, 331, lower di= ag =3D 7795, upper diag =3D 7795) Length: 17

Seed<Simple, TCon= fig>(8169, 363, 8181, 375, lower diag =3D 7806, upper diag =3D 7806) Len= gth: 12

Seed<Simple, TConfig>(8208, 381, 8222, 395, lower d= iag =3D 7827, upper diag =3D 7827) Length: 14

Seed<Simple, TCo= nfig>(8222, 402, 8234, 414, lower diag =3D 7820, upper diag =3D 7820) Le= ngth: 12

Seed<Simple, TConfig>(8287, 446, 8304, 463, lower = diag =3D 7841, upper diag =3D 7841) Length: 17

Seed<Simple, TC= onfig>(8304, 466, 8316, 478, lower diag =3D 7838, upper diag =3D 7838) L= ength: 12

Seed<Simple, TConfig>(8326, 748, 8338, 760, lower= diag =3D 7578, upper diag =3D 7578) Length: 12

Seed<Simple, T= Config>(8354, 761, 8366, 773, lower diag =3D 7593, upper diag =3D 7593) = Length: 12

Seed<Simple, TConfig>(8426, 801, 8438, 813, lowe= r diag =3D 7625, upper diag =3D 7625) Length: 12

Seed<Simple, = TConfig>(8702, 2291, 8721, 2310, lower diag =3D 6411, upper diag =3D 641= 1) Length: 19

Seed<Simple, TConfig>(8769, 2314, 8781, 2326,= lower diag =3D 6455, upper diag =3D 6455) Length: 12

Seed<Sim= ple, TConfig>(8794, 2387, 8806, 2399, lower diag =3D 6407, upper diag = =3D 6407) Length: 12

Seed<Simple, TConfig>(8835, 2400, 8847= , 2412, lower diag =3D 6435, upper diag =3D 6435) Length: 12

Seed= <Simple, TConfig>(9162, 2650, 9174, 2662, lower diag =3D 6512, upper = diag =3D 6512) Length: 12

Seed<Simple, TConfig>(9184, 2676,= 9196, 2688, lower diag =3D 6508, upper diag =3D 6508) Length: 12

Seed<Simple, TConfig>(9196, 2736, 9208, 2748, lower diag =3D 6460, u= pper diag =3D 6460) Length: 12

Seed<Simple, TConfig>(9223, = 2818, 9235, 2830, lower diag =3D 6405, upper diag =3D 6405) Length: 12

Seed<Simple, TConfig>(9251, 2844, 9267, 2860, lower diag =3D 64= 07, upper diag =3D 6407) Length: 16

Seed<Simple, TConfig>(9= 294, 2871, 9308, 2885, lower diag =3D 6423, upper diag =3D 6423) Length: 14=

Seed<Simple, TConfig>(9314, 2891, 9327, 2904, lower diag = =3D 6423, upper diag =3D 6423) Length: 13

Seed<Simple, TConfig= >(9432, 2976, 9447, 2991, lower diag =3D 6456, upper diag =3D 6456) Leng= th: 15

Seed<Simple, TConfig>(9515, 2992, 9527, 3004, lower = diag =3D 6523, upper diag =3D 6523) Length: 12

Seed<Simple, TC= onfig>(9675, 3385, 9701, 3411, lower diag =3D 6290, upper diag =3D 6290)= Length: 26

Seed<Simple, TConfig>(9724, 3414, 9736, 3426, l= ower diag =3D 6310, upper diag =3D 6310) Length: 12

Seed<Simpl= e, TConfig>(9791, 3571, 9804, 3584, lower diag =3D 6220, upper diag =3D = 6220) Length: 13

Seed<Simple, TConfig>(9805, 3596, 9817, 36= 08, lower diag =3D 6209, upper diag =3D 6209) Length: 12

Seed<= Simple, TConfig>(9818, 4915, 9830, 4927, lower diag =3D 4903, upper diag= =3D 4903) Length: 12

Seed<Simple, TConfig>(9842, 4939, 985= 4, 4951, lower diag =3D 4903, upper diag =3D 4903) Length: 12

See= d<Simple, TConfig>(9873, 5045, 9885, 5057, lower diag =3D 4828, upper= diag =3D 4828) Length: 12

Seed<Simple, TConfig>(9886, 5077= , 9898, 5089, lower diag =3D 4809, upper diag =3D 4809) Length: 12

Seed<Simple, TConfig>(9943, 5242, 9955, 5254, lower diag =3D 4701, = upper diag =3D 4701) Length: 12

Seed<Simple, TConfig>(9957,= 5385, 9969, 5397, lower diag =3D 4572, upper diag =3D 4572) Length: 12

Seed<Simple, TConfig>(9994, 5423, 10006, 5435, lower diag =3D = 4571, upper diag =3D 4571) Length: 12

Seed<Simple, TConfig>= (10062, 7096, 10074, 7108, lower diag =3D 2966, upper diag =3D 2966) Length= : 12

Seed<Simple, TConfig>(10102, 7109, 10114, 7121, lower = diag =3D 2993, upper diag =3D 2993) Length: 12

Seed<Simple, TC= onfig>(10156, 7131, 10178, 7153, lower diag =3D 3025, upper diag =3D 302= 5) Length: 22

Seed<Simple, TConfig>(10277, 7354, 10299, 737= 6, lower diag =3D 2923, upper diag =3D 2923) Length: 22

Seed<S= imple, TConfig>(10299, 7378, 10313, 7392, lower diag =3D 2921, upper dia= g =3D 2921) Length: 14

Seed<Simple, TConfig>(10371, 7400, 1= 0385, 7414, lower diag =3D 2971, upper diag =3D 2971) Length: 14

"""

-Brett

= On Sun, Nov 16, 2014 at 2:57 AM, Rahn, Ren=C3=A9 <rene.maerker@fu-= berlin.de> wrote:

Hey Brett,=C2=A0

It could have multiple reasons.=C2=A0

In general, it means that there was a traceback path from a seed or a = gap, that couldn=E2=80=99t be connected with one of the so far generated tr= aceback paths. Note, that the traceback is computed incrementally to reduce= the space requirements.=C2=A0

If you could send me a simple text file containing the seeds of the se= ed chain (one seed per row using the <<-operator), that is input to t= he banded chain alignment function, I could have a look at it and fix the p= roblem.=C2=A0

Also, I opened an issue in github:=C2=A0https://github.com/seqan/seqan/is= sues/699, for tracking the issue.

Kind regards,=C2=A0

Ren=C3=A9 Rahn

On 16 Nov 2014, at 04:17, Brett Bowman <bnbowman@gmail.com> wrote:

I'm trying to build a tool with=C2=A0SeqAn= =C2=A0to quickly align some PacBio data, using "bandedChainAlignment", bu= t I'm consistently getting a crash during the trace-back step.=C2=A0 Th= e generation of the Seeds (SuffixArray) and the finding of the base SeedCha= in works fine, but the final step of turning that into an alignment doesn't appear to work. =C2=A0

Suggestions?

Error Log:

"""

bbowman@localhost:~/git/SRSLI$ ./src/C++/srsli test/data/query/ecoli_5= p_sample.fastq test/data/reference/ecoliK12_5p_assembly.fasta=C2=A0

Query 0

Finished finding seeds

Finishing chaining seeds

Starting alignment of sequences

/usr/include/seqan/= seeds/banded_chain_alignment_traceback.h:195 Assertion failed : isGlued =3D= =3D true was: 0 !=3D 1 (Fatal error while trying to connect trace backs: No= glue point available!)

Aborted (core dumped)

"""

-Brett

_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

---

Ren=C3=A9 Rahn

Ph.D. Student

--------------------------------

Tel: =C2=A0(+49) 30 838 75277=

Mail:=C2=A0rene.rahn@fu-berlin.de

--------------------------------

Institute of Computer Science

Algorithmic Bioinformatics (ABI)
--------------------------------
Freie Universit=C3=A4t Berlin

Takustra=C3=9Fe 9

14195 Berlin

--------------------------------

_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev

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Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XqH6X-003DFG-8f>; Mon, 17 Nov 2014 08:52:09 +0100 Received: from mail-yk0-f178.google.com ([209.85.160.178]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XqH6W-000qwR-UP>; Mon, 17 Nov 2014 08:52:09 +0100 Received: by mail-yk0-f178.google.com with SMTP id 20so2696209yks.37 for ; Sun, 16 Nov 2014 23:52:06 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=dGqT9d1odCRFa0KezdZ7VoSHhLV6aVwNTUsWjDc5GnI=; b=Dk+ZDAZb8jf8ZuOGFpVhTb2/TWEwUoiz6iAzwE4fmFoe2akNNO+quFj+xU3A8kRzq7 QTc/G6hPb41gvyIyb9lEjdHkCk17kKt30s454YHTMAbY7PittyfyHd5J8WT1ClZmAk1T LMl6hm29qFnUSfliLQm7yLqNc5OBtRAdBT4jAS39VlqtlmSM+d3A1hT5Pg19ktUnXmty HJQdSxkjg7tUqEGH9gZHOd4kcLkKSM2Yv+bytYn8axH/kN5dJYX5LNmjKou4X8ve8Qfs bzkG3mvng4ptvzRxUhHiLJvKPM5iz9/CM4RpWIJrUXMxh8Ivn0iAWnMdoLsiGQRaa+0Z ACsQ== MIME-Version: 1.0 X-Received: by 10.170.98.84 with SMTP id p81mr965564yka.40.1416210726514; Sun, 16 Nov 2014 23:52:06 -0800 (PST) Received: by 10.170.110.19 with HTTP; Sun, 16 Nov 2014 23:52:06 -0800 (PST) In-Reply-To: References: <50D46377-BAED-47B3-8091-6DF539B7C9E8@fritz.box> Date: Sun, 16 Nov 2014 23:52:06 -0800 Message-ID: From: Brett Bowman To: SeqAn Development Content-Type: multipart/alternative; boundary=001a113aae4447f6f7050809416a X-Originating-IP: 209.85.160.178 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416210729-00067E64-AF3E4510/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.086188, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Fatal Error in Banded Chain Alignment Traceback X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 17 Nov 2014 07:52:11 -0000 --001a113aae4447f6f7050809416a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable I've gotten a rudimentary alignment out, but I had to tweak a few things: """ 0 . : . : . : . : . : AAAGAG--AGAGAT-ATGCCAGTAATA-CTTGAAAGATATTGCCGAGCTG | | | || |||||||||||| |||||||||||||||||||||| ---GTGCCCGTCATAATGCCAGTAATAGCTTGAAAGATATTGCCGAGCTG 50 . : . : . : . : . : GTGCCGTTTGCCCATCGTTATGGTGCAAAAA-TTTCGTCACGCTTAACAC ||||||||||||||||||||||||||||||| |||||||||||||||||| GTGCCGTTTGCCCATCGTTATGGTGCAAAAATTTTCGTCACGCTTAACAC 100 . : . : . : . : . : CATTTTGCATGATGATGAGCTGGAACCCGCGC-ACGGCTGATTACTGACC |||||||||||||||||||||||||||||||| ||||||||||||||||| CATTTTGCATGATGATGAGCTGGAACCCGCGCAACGGCTGATTACTGACC 150 . : . : . : . : . : TCTACCAGACCGGTGTCGATGCGCTGATTGTT-AGGATATGGGGATTCTG |||||||||||||||||||||||||||||||| ||||||||||||||||| TCTACCAGACCGGTGTCGATGCGCTGATTGTTCAGGATATGGGGATTCTG 200 . : . : . : . : . : GAAACCTTGATATTCGCGCGCGATTGAACTGGCACGCCAGTACCGCAGTG | || |||||||||| ||| |||||||||| ||||||||||| ||||||| G-AA-CTTGATATTC-CGC-CGATTGAACT-GCACGCCAGTA-CGCAGTG """ The scoring scheme had to be changed from: Score scoringScheme(4, -13, -7); // Determined empirically to work well on PacBio data with my home-brewed aligner to: Score scoringScheme(2, -1, -2); // Scoring scheme recommended/tested by SeqAn docs The initial Seed-set had to be set by hand with the reference-alignment's start position: SeedSet seeds2; addSeed(seeds2, TSeed( 12, 12, 100), seqan::Single()); addSeed(seeds2, TSeed( 120, 120, 100), seqan::Single()); So it appears that there are at least two issues at play here: -The value-type used for the bandedChainAlignment isn't large enough to handle multi-kb alignments with moderate-sized penalties -The default chaining algorithm doesn't handle large numbers of seeds with small indel gaps well. -Brett On Sun, Nov 16, 2014 at 9:39 PM, Brett Bowman wrote: > Thanks Rene, > > My query, reference, and canonical alignment from BLASR (the > PacBio-specific aligner) attached. > > I also noticed that the seeds it's chaining with chainGlobalAlignment() > are way off the diagonal, which may be related - details below: > > """ > Query #1 - > m130404_014004_sidney_c100506902550000001823076808221337_s1_p0/5779/0_103= 97 > Finished finding seeds > Seeds: 1939 > Finishing chaining seeds > Chain: 44 > Seed(7688, 57, 7706, 75, lower diag =3D 7631, upper diag= =3D > 7631) Length: 18 > Seed(7707, 94, 7722, 109, lower diag =3D 7613, upper dia= g =3D > 7613) Length: 15 > Seed(7933, 111, 7946, 124, lower diag =3D 7822, upper di= ag > =3D 7822) Length: 13 > Seed(7949, 130, 7965, 146, lower diag =3D 7819, upper di= ag > =3D 7819) Length: 16 > Seed(8065, 299, 8078, 312, lower diag =3D 7766, upper di= ag > =3D 7766) Length: 13 > Seed(8109, 314, 8126, 331, lower diag =3D 7795, upper di= ag > =3D 7795) Length: 17 > Seed(8169, 363, 8181, 375, lower diag =3D 7806, upper di= ag > =3D 7806) Length: 12 > Seed(8208, 381, 8222, 395, lower diag =3D 7827, upper di= ag > =3D 7827) Length: 14 > Seed(8222, 402, 8234, 414, lower diag =3D 7820, upper di= ag > =3D 7820) Length: 12 > Seed(8287, 446, 8304, 463, lower diag =3D 7841, upper di= ag > =3D 7841) Length: 17 > Seed(8304, 466, 8316, 478, lower diag =3D 7838, upper di= ag > =3D 7838) Length: 12 > Seed(8326, 748, 8338, 760, lower diag =3D 7578, upper di= ag > =3D 7578) Length: 12 > Seed(8354, 761, 8366, 773, lower diag =3D 7593, upper di= ag > =3D 7593) Length: 12 > Seed(8426, 801, 8438, 813, lower diag =3D 7625, upper di= ag > =3D 7625) Length: 12 > Seed(8702, 2291, 8721, 2310, lower diag =3D 6411, upper > diag =3D 6411) Length: 19 > Seed(8769, 2314, 8781, 2326, lower diag =3D 6455, upper > diag =3D 6455) Length: 12 > Seed(8794, 2387, 8806, 2399, lower diag =3D 6407, upper > diag =3D 6407) Length: 12 > Seed(8835, 2400, 8847, 2412, lower diag =3D 6435, upper > diag =3D 6435) Length: 12 > Seed(9162, 2650, 9174, 2662, lower diag =3D 6512, upper > diag =3D 6512) Length: 12 > Seed(9184, 2676, 9196, 2688, lower diag =3D 6508, upper > diag =3D 6508) Length: 12 > Seed(9196, 2736, 9208, 2748, lower diag =3D 6460, upper > diag =3D 6460) Length: 12 > Seed(9223, 2818, 9235, 2830, lower diag =3D 6405, upper > diag =3D 6405) Length: 12 > Seed(9251, 2844, 9267, 2860, lower diag =3D 6407, upper > diag =3D 6407) Length: 16 > Seed(9294, 2871, 9308, 2885, lower diag =3D 6423, upper > diag =3D 6423) Length: 14 > Seed(9314, 2891, 9327, 2904, lower diag =3D 6423, upper > diag =3D 6423) Length: 13 > Seed(9432, 2976, 9447, 2991, lower diag =3D 6456, upper > diag =3D 6456) Length: 15 > Seed(9515, 2992, 9527, 3004, lower diag =3D 6523, upper > diag =3D 6523) Length: 12 > Seed(9675, 3385, 9701, 3411, lower diag =3D 6290, upper > diag =3D 6290) Length: 26 > Seed(9724, 3414, 9736, 3426, lower diag =3D 6310, upper > diag =3D 6310) Length: 12 > Seed(9791, 3571, 9804, 3584, lower diag =3D 6220, upper > diag =3D 6220) Length: 13 > Seed(9805, 3596, 9817, 3608, lower diag =3D 6209, upper > diag =3D 6209) Length: 12 > Seed(9818, 4915, 9830, 4927, lower diag =3D 4903, upper > diag =3D 4903) Length: 12 > Seed(9842, 4939, 9854, 4951, lower diag =3D 4903, upper > diag =3D 4903) Length: 12 > Seed(9873, 5045, 9885, 5057, lower diag =3D 4828, upper > diag =3D 4828) Length: 12 > Seed(9886, 5077, 9898, 5089, lower diag =3D 4809, upper > diag =3D 4809) Length: 12 > Seed(9943, 5242, 9955, 5254, lower diag =3D 4701, upper > diag =3D 4701) Length: 12 > Seed(9957, 5385, 9969, 5397, lower diag =3D 4572, upper > diag =3D 4572) Length: 12 > Seed(9994, 5423, 10006, 5435, lower diag =3D 4571, upper > diag =3D 4571) Length: 12 > Seed(10062, 7096, 10074, 7108, lower diag =3D 2966, uppe= r > diag =3D 2966) Length: 12 > Seed(10102, 7109, 10114, 7121, lower diag =3D 2993, uppe= r > diag =3D 2993) Length: 12 > Seed(10156, 7131, 10178, 7153, lower diag =3D 3025, uppe= r > diag =3D 3025) Length: 22 > Seed(10277, 7354, 10299, 7376, lower diag =3D 2923, uppe= r > diag =3D 2923) Length: 22 > Seed(10299, 7378, 10313, 7392, lower diag =3D 2921, uppe= r > diag =3D 2921) Length: 14 > Seed(10371, 7400, 10385, 7414, lower diag =3D 2971, uppe= r > diag =3D 2971) Length: 14 > """ > > -Brett > > On Sun, Nov 16, 2014 at 2:57 AM, Rahn, Ren=C3=A9 > wrote: > >> Hey Brett, >> >> It could have multiple reasons. >> In general, it means that there was a traceback path from a seed or a >> gap, that couldn=E2=80=99t be connected with one of the so far generated= traceback >> paths. Note, that the traceback is computed incrementally to reduce the >> space requirements. >> If you could send me a simple text file containing the seeds of the seed >> chain (one seed per row using the <<-operator), that is input to the ban= ded >> chain alignment function, I could have a look at it and fix the problem. >> Also, I opened an issue in github: >> https://github.com/seqan/seqan/issues/699, for tracking the issue. >> >> >> Kind regards, >> >> Ren=C3=A9 Rahn >> >> On 16 Nov 2014, at 04:17, Brett Bowman wrote: >> >> I'm trying to build a tool with SeqAn to quickly align some PacBio >> data, using "bandedChainAlignment", but I'm consistently getting a crash >> during the trace-back step. The generation of the Seeds (SuffixArray) a= nd >> the finding of the base SeedChain works fine, but the final step of turn= ing >> that into an alignment doesn't appear to work. >> >> Suggestions? >> >> Error Log: >> """ >> bbowman@localhost:~/git/SRSLI$ ./src/C++/srsli >> test/data/query/ecoli_5p_sample.fastq >> test/data/reference/ecoliK12_5p_assembly.fasta >> Query 0 >> Finished finding seeds >> Finishing chaining seeds >> Starting alignment of sequences >> /usr/include/seqan/seeds/banded_chain_alignment_traceback.h:195 >> Assertion failed : isGlued =3D=3D true was: 0 !=3D 1 (Fatal error while = trying to >> connect trace backs: No glue point available!) >> Aborted (core dumped) >> """ >> >> -Brett >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >> >> >> --- >> >> Ren=C3=A9 Rahn >> Ph.D. Student >> -------------------------------- >> Tel: (+49) 30 838 75277 >> Mail: rene.rahn@fu-berlin.de >> -------------------------------- >> Institute of Computer Science >> Algorithmic Bioinformatics (ABI) >> -------------------------------- >> Freie Universit=C3=A4t Berlin >> Takustra=C3=9Fe 9 >> 14195 Berlin >> -------------------------------- >> >> >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev >> >> > --001a113aae4447f6f7050809416a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

I've gotten a rudimentary alignment out, but I ha= d to tweak a few things:

"""

<= div>

=C2=A0 =C2=A0 =C2=A0 0 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2= =A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2= =A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0:=C2=A0

=C2=A0 =C2=A0 =C2=A0 =C2= =A0 AAAGAG--AGAGAT-ATGCCAGTAATA-CTTGAAAGATATTGCCGAGCTG

=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0| | =C2=A0 | =C2=A0|| |||||||||||| |||||||||= |||||||||||||

=C2=A0 =C2=A0 =C2=A0 =C2=A0 ---GTGCCCGTCATAATGCCAGT= AATAGCTTGAAAGATATTGCCGAGCTG

=C2=A0 =C2=A0 =C2=A050= =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0= . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0= :=C2=A0

=C2=A0 =C2=A0 =C2=A0 =C2=A0 GTGCCGTTTGCCCATCGTTATGGTGCAAA= AA-TTTCGTCACGCTTAACAC

=C2=A0 =C2=A0 =C2=A0 =C2=A0 |||||||||||||||= |||||||||||||||| ||||||||||||||||||

=C2=A0 =C2=A0 =C2=A0 =C2=A0 G= TGCCGTTTGCCCATCGTTATGGTGCAAAAATTTTCGTCACGCTTAACAC

= =C2=A0 =C2=A0 100 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2= =A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2= =A0. =C2=A0 =C2=A0:=C2=A0

=C2=A0 =C2=A0 =C2=A0 =C2=A0 CATTTTGCATG= ATGATGAGCTGGAACCCGCGC-ACGGCTGATTACTGACC

=C2=A0 =C2=A0 =C2=A0 =C2= =A0 |||||||||||||||||||||||||||||||| |||||||||||||||||

=C2=A0 =C2= =A0 =C2=A0 =C2=A0 CATTTTGCATGATGATGAGCTGGAACCCGCGCAACGGCTGATTACTGACC

<= div>

=C2=A0 =C2=A0 150 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 = =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 = =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0:=C2=A0

=C2=A0 =C2=A0 =C2=A0 = =C2=A0 TCTACCAGACCGGTGTCGATGCGCTGATTGTT-AGGATATGGGGATTCTG

=C2=A0 = =C2=A0 =C2=A0 =C2=A0 |||||||||||||||||||||||||||||||| |||||||||||||||||

=C2=A0 =C2=A0 =C2=A0 =C2=A0 TCTACCAGACCGGTGTCGATGCGCTGATTGTTCAGGATAT= GGGGATTCTG

=C2=A0 =C2=A0 200 =C2=A0 =C2=A0 . =C2= =A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2= =A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0:=C2=A0

= =C2=A0 =C2=A0 =C2=A0 =C2=A0 GAAACCTTGATATTCGCGCGCGATTGAACTGGCACGCCAGTACCGCA= GTG

=C2=A0 =C2=A0 =C2=A0 =C2=A0 | || |||||||||| ||| |||||||||| ||= ||||||||| |||||||

=C2=A0 =C2=A0 =C2=A0 =C2=A0 G-AA-CTTGATATTC-CGC= -CGATTGAACT-GCACGCCAGTA-CGCAGTG

"""

The scoring scheme had to be changed from:

= Score<short, Simple> scoringScheme(4, -13, -7); =C2=A0 // Determined = empirically to work well on PacBio data with my home-brewed aligner

to:

Score<short, Simple> scoringScheme(2, -1, -2); =C2= =A0 =C2=A0 // Scoring scheme recommended/tested by SeqAn docs

On Tue, Nov 18, 2014 at 7:25 AM, Rahn, R= en=C3=A9 <rene.maerker@fu-berlin.de> wrote:

Sorry,=C2=A0

On 18 Nov 2014, at 16:19, Rahn, Ren=C3=A9 <rene.maerker@fu-berlin.de> wr= ote:

Hey Brett,=C2=A0

by just looking at the seed chain I might think that the problem is th= e bad chain in the first place.

The first seed begins at position 7688 for the first sequence, while t= he seed for the second sequence starts at position 57.=C2=A0

There I can have at most 57 matches and have 7631 gaps. Given a score = of -7 for the gaps and 4 for the matches I have a score of at least -53189 = which in fact exceeds the bound of

unsigned shorts -32.768 - 32.767.

I meant signed shorts of course :).

This would also explain why it works with a gap penalty of -2 ~ -15300= .

Using unsigned short cannot give correct results, as it is only define= d on the values from 0 to 65535. In this case -7 would also be interpreted = as=C2=A065529.

So somewhere in the first matrix is an overflow, which might lead to t= he problem with the traceback. I will investigate this more thoroughly in t= he next days.=C2=A0

For the moment I suggest 2 things.=C2=A0

A) Try to use signed integer types and see if it runs through. (Just t= o check if it is really related to the value overflow.)

B) Use chaos chaining when adding seeds to the seed set. From the data= set I would guess you used the simple merge strategy, but given that the s= equences might not be =E2=80=9Cvery=E2=80=9D similar the chaos chaining mig= ht compute better results and then the banded chain alignment might work as well.

Did you changed the default band settings for the band width of the ba= ndedChainAlignment (this parameter k)?

Cheers,

Ren=C3=A9

On 18 Nov 2014, at 02:17, Brett Bowman <bnbowman@gmail.com> wrote:

Opps, I just not= iced a mistake in my previous e-mail.=C2=A0 I wrote:

""&quo= t;

The scoring sche= me had to be changed from:

Score<short, Simple> scoringScheme(4, -13, -7); =C2=A0 // Determ= ined empirically to work well on PacBio data with my home-brewed aligner
to:

Score<short, Simple> scoringScheme(2, -1, -2); =C2=A0 =C2=A0 // = Scoring scheme recommended/tested by=C2=A0SeqAn=C2=A0docs
"""

but what I meant was (changes in CAPITAL):

"""

The scoring scheme had to be changed from:

Score<UNSIGNED short, Simple> scoringScheme(4, -13, -7); =C2=A0 = // Determined empirically to work well on PacBio data with my home-brewed a= ligner

to:

Score<UNSIGNED short, Simple> scoringScheme(2, -1, -2); =C2=A0 = =C2=A0 // Scoring scheme recommended/tested by=C2=A0SeqAn=C2= =A0docs

"""

I was not surprised when regular shorts were not large enough given th= at we're dealing with ~10kb alignments, but I was surprised that unsign= ed shorts did not work.=C2=A0 They are preferable given their smaller size,= and used by some of my home-brewed aligners.=C2=A0

-Brett

On Sun, Nov 16, 2014 at 11:52 PM, Brett Bowman <= span dir=3D"ltr"> <bnbowman@gmail.= com> wrote:

I've gotten a rudimentary alignment out, but I had to tweak a few = things:

"""

=C2=A0 =C2=A0 =C2=A0 0 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. = =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: = =C2=A0 =C2=A0. =C2=A0 =C2=A0:=C2=A0

=C2=A0 =C2=A0 =C2=A0 =C2=A0 AAAGAG--AGAGAT-ATGCCAGTAATA-CTTGAAAGATATTG= CCGAGCTG

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0| | =C2=A0 | =C2=A0|| |||||||= ||||| ||||||||||||||||||||||

=C2=A0 =C2=A0 =C2=A0 =C2=A0 ---GTGCCCGTCATAATGCCAGTAATAGCTTGAAAGATATTG= CCGAGCTG

=C2=A0 =C2=A0 =C2=A050 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. = =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: = =C2=A0 =C2=A0. =C2=A0 =C2=A0:=C2=A0

=C2=A0 =C2=A0 =C2=A0 =C2=A0 GTGCCGTTTGCCCATCGTTATGGTGCAAAAA-TTTCGTCACG= CTTAACAC

=C2=A0 =C2=A0 =C2=A0 =C2=A0 ||||||||||||||||||||||||||||||| ||||||||||= ||||||||

=C2=A0 =C2=A0 =C2=A0 =C2=A0 GTGCCGTTTGCCCATCGTTATGGTGCAAAAATTTTCGTCACG= CTTAACAC

=C2=A0 =C2=A0 100 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0= =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0= =C2=A0. =C2=A0 =C2=A0:=C2=A0

=C2=A0 =C2=A0 =C2=A0 =C2=A0 CATTTTGCATGATGATGAGCTGGAACCCGCGC-ACGGCTGAT= TACTGACC

=C2=A0 =C2=A0 =C2=A0 =C2=A0 |||||||||||||||||||||||||||||||| |||||||||= ||||||||

=C2=A0 =C2=A0 =C2=A0 =C2=A0 CATTTTGCATGATGATGAGCTGGAACCCGCGCAACGGCTGAT= TACTGACC

=C2=A0 =C2=A0 150 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0= =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0= =C2=A0. =C2=A0 =C2=A0:=C2=A0

=C2=A0 =C2=A0 =C2=A0 =C2=A0 TCTACCAGACCGGTGTCGATGCGCTGATTGTT-AGGATATGG= GGATTCTG

=C2=A0 =C2=A0 =C2=A0 =C2=A0 |||||||||||||||||||||||||||||||| |||||||||= ||||||||

=C2=A0 =C2=A0 =C2=A0 =C2=A0 TCTACCAGACCGGTGTCGATGCGCTGATTGTTCAGGATATGG= GGATTCTG

=C2=A0 =C2=A0 200 =C2=A0 =C2=A0 . =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0= =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0 =C2=A0. =C2=A0 =C2=A0: =C2=A0= =C2=A0. =C2=A0 =C2=A0:=C2=A0

=C2=A0 =C2=A0 =C2=A0 =C2=A0 GAAACCTTGATATTCGCGCGCGATTGAACTGGCACGCCAGTA= CCGCAGTG

=C2=A0 =C2=A0 =C2=A0 =C2=A0 | || |||||||||| ||| |||||||||| |||||||||||= |||||||

=C2=A0 =C2=A0 =C2=A0 =C2=A0 G-AA-CTTGATATTC-CGC-CGATTGAACT-GCACGCCAGTA= -CGCAGTG

"""

The scoring scheme had to be changed from:

Score<short, Simple> scoringScheme(4, -13, -7); =C2=A0 // Determ= ined empirically to work well on PacBio data with my home-brewed aligner
to:

Score<short, Simple> scoringScheme(2, -1, -2); =C2=A0 =C2=A0 // = Scoring scheme recommended/tested by SeqAn docs

The initial Seed-set had to be set by hand with the reference-alignmen= t's start position:

SeedSet<Simple> seeds2;

addSeed(seeds2, TSeed( =C2=A012, =C2=A0 12, 100), seqan::Single());
addSeed(seeds2, TSeed( 120, =C2=A0120, 100), seqan::Single());

So it appears that there are at least two issues at play here:

-The value-type used for the bandedChainAlignment isn't large enou= gh to handle multi-kb alignments with moderate-sized penalties

-The default chaining algorithm doesn't handle large numbers of se= eds with small indel gaps well.

-Brett

On Sun, Nov 16, 2014 at 9:39 PM, Brett Bowman <bnbowman@gmail.= com> wrote:

Thanks Rene,

My query, reference, and canonical alignment from BLASR (the PacBio-specifi= c aligner) attached.

I also noticed that the seeds it's chaining with chainGlobalAlignm= ent() are way off the diagonal, which may be related - details below:=C2=A0=

"""

Query #1 - m130404_014004_sidney_c100506902550000001823076808221337_s1= _p0/5779/0_10397

Finished finding seeds

Seeds: 1939

Finishing chaining seeds

Chain: 44

Seed<Simple, TConfig>(7688, 57, 7706, 75, lower diag =3D 7631, u= pper diag =3D 7631) Length: 18

Seed<Simple, TConfig>(7707, 94, 7722, 109, lower diag =3D 7613, = upper diag =3D 7613) Length: 15

Seed<Simple, TConfig>(7933, 111, 7946, 124, lower diag =3D 7822,= upper diag =3D 7822) Length: 13

Seed<Simple, TConfig>(7949, 130, 7965, 146, lower diag =3D 7819,= upper diag =3D 7819) Length: 16

Seed<Simple, TConfig>(8065, 299, 8078, 312, lower diag =3D 7766,= upper diag =3D 7766) Length: 13

Seed<Simple, TConfig>(8109, 314, 8126, 331, lower diag =3D 7795,= upper diag =3D 7795) Length: 17

Seed<Simple, TConfig>(8169, 363, 8181, 375, lower diag =3D 7806,= upper diag =3D 7806) Length: 12

Seed<Simple, TConfig>(8208, 381, 8222, 395, lower diag =3D 7827,= upper diag =3D 7827) Length: 14

Seed<Simple, TConfig>(8222, 402, 8234, 414, lower diag =3D 7820,= upper diag =3D 7820) Length: 12

Seed<Simple, TConfig>(8287, 446, 8304, 463, lower diag =3D 7841,= upper diag =3D 7841) Length: 17

Seed<Simple, TConfig>(8304, 466, 8316, 478, lower diag =3D 7838,= upper diag =3D 7838) Length: 12

Seed<Simple, TConfig>(8326, 748, 8338, 760, lower diag =3D 7578,= upper diag =3D 7578) Length: 12

Seed<Simple, TConfig>(8354, 761, 8366, 773, lower diag =3D 7593,= upper diag =3D 7593) Length: 12

Seed<Simple, TConfig>(8426, 801, 8438, 813, lower diag =3D 7625,= upper diag =3D 7625) Length: 12

Seed<Simple, TConfig>(8702, 2291, 8721, 2310, lower diag =3D 641= 1, upper diag =3D 6411) Length: 19

Seed<Simple, TConfig>(8769, 2314, 8781, 2326, lower diag =3D 645= 5, upper diag =3D 6455) Length: 12

Seed<Simple, TConfig>(8794, 2387, 8806, 2399, lower diag =3D 640= 7, upper diag =3D 6407) Length: 12

Seed<Simple, TConfig>(8835, 2400, 8847, 2412, lower diag =3D 643= 5, upper diag =3D 6435) Length: 12

Seed<Simple, TConfig>(9162, 2650, 9174, 2662, lower diag =3D 651= 2, upper diag =3D 6512) Length: 12

Seed<Simple, TConfig>(9184, 2676, 9196, 2688, lower diag =3D 650= 8, upper diag =3D 6508) Length: 12

Seed<Simple, TConfig>(9196, 2736, 9208, 2748, lower diag =3D 646= 0, upper diag =3D 6460) Length: 12

Seed<Simple, TConfig>(9223, 2818, 9235, 2830, lower diag =3D 640= 5, upper diag =3D 6405) Length: 12

Seed<Simple, TConfig>(9251, 2844, 9267, 2860, lower diag =3D 640= 7, upper diag =3D 6407) Length: 16

Seed<Simple, TConfig>(9294, 2871, 9308, 2885, lower diag =3D 642= 3, upper diag =3D 6423) Length: 14

Seed<Simple, TConfig>(9314, 2891, 9327, 2904, lower diag =3D 642= 3, upper diag =3D 6423) Length: 13

Seed<Simple, TConfig>(9432, 2976, 9447, 2991, lower diag =3D 645= 6, upper diag =3D 6456) Length: 15

Seed<Simple, TConfig>(9515, 2992, 9527, 3004, lower diag =3D 652= 3, upper diag =3D 6523) Length: 12

Seed<Simple, TConfig>(9675, 3385, 9701, 3411, lower diag =3D 629= 0, upper diag =3D 6290) Length: 26

Seed<Simple, TConfig>(9724, 3414, 9736, 3426, lower diag =3D 631= 0, upper diag =3D 6310) Length: 12

Seed<Simple, TConfig>(9791, 3571, 9804, 3584, lower diag =3D 622= 0, upper diag =3D 6220) Length: 13

Seed<Simple, TConfig>(9805, 3596, 9817, 3608, lower diag =3D 620= 9, upper diag =3D 6209) Length: 12

Seed<Simple, TConfig>(9818, 4915, 9830, 4927, lower diag =3D 490= 3, upper diag =3D 4903) Length: 12

Seed<Simple, TConfig>(9842, 4939, 9854, 4951, lower diag =3D 490= 3, upper diag =3D 4903) Length: 12

Seed<Simple, TConfig>(9873, 5045, 9885, 5057, lower diag =3D 482= 8, upper diag =3D 4828) Length: 12

Seed<Simple, TConfig>(9886, 5077, 9898, 5089, lower diag =3D 480= 9, upper diag =3D 4809) Length: 12

Seed<Simple, TConfig>(9943, 5242, 9955, 5254, lower diag =3D 470= 1, upper diag =3D 4701) Length: 12

Seed<Simple, TConfig>(9957, 5385, 9969, 5397, lower diag =3D 457= 2, upper diag =3D 4572) Length: 12

Seed<Simple, TConfig>(9994, 5423, 10006, 5435, lower diag =3D 45= 71, upper diag =3D 4571) Length: 12

Seed<Simple, TConfig>(10062, 7096, 10074, 7108, lower diag =3D 2= 966, upper diag =3D 2966) Length: 12

Seed<Simple, TConfig>(10102, 7109, 10114, 7121, lower diag =3D 2= 993, upper diag =3D 2993) Length: 12

Seed<Simple, TConfig>(10156, 7131, 10178, 7153, lower diag =3D 3= 025, upper diag =3D 3025) Length: 22

Seed<Simple, TConfig>(10277, 7354, 10299, 7376, lower diag =3D 2= 923, upper diag =3D 2923) Length: 22

Seed<Simple, TConfig>(10299, 7378, 10313, 7392, lower diag =3D 2= 921, upper diag =3D 2921) Length: 14

Seed<Simple, TConfig>(10371, 7400, 10385, 7414, lower diag =3D 2= 971, upper diag =3D 2971) Length: 14

"""

-Brett

On Sun, Nov 16, 2014 at 2:57 AM, Rahn, Ren=C3=A9= <rene.mae= rker@fu-berlin.de> wrote:

Hey Brett,=C2=A0

It could have multiple reasons.=C2=A0

In general, it means that there was a traceback path from a seed or a = gap, that couldn=E2=80=99t be connected with one of the so far generated tr= aceback paths. Note, that the traceback is computed incrementally to reduce= the space requirements.=C2=A0

If you could send me a simple text file containing the seeds of the se= ed chain (one seed per row using the <<-operator), that is input to t= he banded chain alignment function, I could have a look at it and fix the p= roblem.=C2=A0

Also, I opened an issue in github:=C2=A0https://github.com/seqan/seqan/is= sues/699, for tracking the issue.

Kind regards,=C2=A0

Ren=C3=A9 Rahn

On 16 Nov 2014, at 04:17, Brett Bowman <bnbowman@gmail.com> wrote:

I'm trying to build a tool with=C2=A0SeqAn= =C2=A0to quickly align some PacBio data, using "bandedChainAlignment", bu= t I'm consistently getting a crash during the trace-back step.=C2=A0 Th= e generation of the Seeds (SuffixArray) and the finding of the base SeedCha= in works fine, but the final step of turning that into an alignment doesn't appear to work. =C2=A0

Suggestions?

Error Log:

"""

bbowman@localhost:~/git/SRSLI$ ./src/C++/srsli test/data/query/ecoli_5= p_sample.fastq test/data/reference/ecoliK12_5p_assembly.fasta=C2=A0

Query 0

Finished finding seeds

Finishing chaining seeds

Starting alignment of sequences

/usr/include/seqan/= seeds/banded_chain_alignment_traceback.h:195 Assertion failed : isGlued =3D= =3D true was: 0 !=3D 1 (Fatal error while trying to connect trace backs: No= glue point available!)

Aborted (core dumped)

"""

-Brett

_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

---

Ren=C3=A9 Rahn

Ph.D. Student

--------------------------------

Tel: =C2=A0(+49) 30 838 75277=

Mail:=C2=A0rene.rahn@fu-berlin.de

--------------------------------

Institute of Computer Science

Algorithmic Bioinformatics (ABI)
--------------------------------
Freie Universit=C3=A4t Berlin

Takustra=C3=9Fe 9

14195 Berlin

--------------------------------

_______________________________________________
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

---

Ren=C3=A9 Rahn

Ph.D. Student

--------------------------------

Tel: =C2=A0(+49) 30 838 75277=

Mail:=C2=A0rene.rahn@fu-berlin.de

--------------------------------

Institute of Computer Science

Algorithmic Bioinformatics (ABI)
--------------------------------
Freie Universit=C3=A4t Berlin

Takustra=C3=9Fe 9

14195 Berlin

--------------------------------

_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

---

Ren=C3=A9 Rahn

Ph.D. Student

--------------------------------

Tel: =C2=A0(+49) 30 838 75277=

Mail:=C2=A0rene.rahn@fu-berlin.de

--------------------------------

Institute of Computer Science

Algorithmic Bioinformatics (ABI)

--------------------------------

Freie Universit=C3=A4t Berlin

Takustra=C3=9Fe 9

14195 Berlin

--------------------------------

_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev

--089e0122a97271faa40508271f9d-- From bnbowman@gmail.com Wed Nov 19 07:34:50 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Xqyqm-001gJr-F0>; Wed, 19 Nov 2014 07:34:48 +0100 Received: from mail-yk0-f180.google.com ([209.85.160.180]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1Xqyqm-000TSi-5s>; Wed, 19 Nov 2014 07:34:48 +0100 Received: by mail-yk0-f180.google.com with SMTP id 9so5757866ykp.25 for ; Tue, 18 Nov 2014 22:34:45 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=qxB2cedsGY88ztpAELdcyGYwnM9kGAMd4mB9Q6CC4gY=; b=anK4iJnaTCggHsI48k+wUyZtGaJbdNVZOXGQUZcY/XLGAo04ZrdS+b9et50MnLy6uR w0M4Fz1SwlbayMh9MzPLSEQubIITmsPJOWoVxpDizC2E9RMJZwlpXVeUI/uGtY2n2RFI hl/Oc2Xgz/+YzfzM6bykX+wxMDAHN5RBRzTtn+RhEv+gJcctX/RcmMXB2NF7ewDgyauX K/a4NQGXvg2GN1VYo6r/AQA0aIJ/BU084oWiliJqeV95jZ3F3ADCeFxlaIHC+3DdflHi NMN4sck56X6p2uUDEPICzTGQ8PxRn2cNiVU/6uBhDNzyZ36XydNO4C//II0qzhVIb800 tBEw== MIME-Version: 1.0 X-Received: by 10.236.228.72 with SMTP id e68mr14000180yhq.56.1416378885398; Tue, 18 Nov 2014 22:34:45 -0800 (PST) Received: by 10.170.110.19 with HTTP; Tue, 18 Nov 2014 22:34:45 -0800 (PST) Date: Tue, 18 Nov 2014 22:34:45 -0800 Message-ID: From: Brett Bowman To: SeqAn Development Content-Type: multipart/alternative; boundary=001a11c2caee54e68e0508306832 X-Originating-IP: 209.85.160.180 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416378888-00067E64-47C87C4B/0/0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.500043, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.8 required=5.0 tests=FREEMAIL_FROM, FU_BOGO_UNSURE, HTML_MESSAGE, RCVD_IN_DNSWL_LOW, RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL, T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Trouble Hashing Kmers into Qgram Index X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 19 Nov 2014 06:34:50 -0000 --001a11c2caee54e68e0508306832 Content-Type: text/plain; charset=UTF-8 Sorry to be a bother, but I decided to go back to the docs and start fresh and I'm still having issues. We're using Qgrams, so I trying to write a simple loop to search for all 12mers from a query sequence "seq" in the index formed from a StringSet of references "refSeq", building on the example code in the Q-Gram Index tutorial: """ TFinder qgramFinder(index); for (size_t i = 0; i < length(seq)-12; i++) { TInfix::Type kmer = infix(seq, i, i+12); std::cout << kmer << std::endl; seqan::hash(indexShape(index), kmer); for (unsigned i = 0; i < length(getOccurrences(index, indexShape(index))); ++i) { std::cout << getOccurrences(index, indexShape(index))[i] << std::endl; } std::cout << std::endl; } """ but I'm getting a fairly obtuse error message I don't quite understand, and doesn't point me back to any specific lines in my code. """ /usr/include/seqan/index/shape_base.h:535:55: error: indirection requires pointer operand ('seqan::Segment, seqan::Alloc >, seqan::InfixSegment>' invalid) hash * ValueSize::VALUE + ordValue((TValue)*it), ^~~ /usr/include/seqan/index/shape_base.h:548:22: note: in instantiation of function template specialization 'seqan::_hashFixedShape, seqan::Segment, seqan::Alloc >, seqan::InfixSegment>, 12>' requested here return me.hValue = _hashFixedShape(me.hValue, it, TValue(), UngappedShape()); ^ /home/bbowman/git/SRSLI/src/C++/SparseAlignment.hpp:102:16: note: in instantiation of function template specialization 'seqan::hash, 12, seqan::Segment, seqan::Alloc >, seqan::InfixSegment> >' requested here seqan::hash(indexShape(index), kmer); ^ /home/bbowman/git/SRSLI/src/C++/main.cpp:86:9: note: in instantiation of function template specialization 'FindSeeds2, seqan::IndexQGram, seqan::Tag > > >' requested here FindSeeds2(querySeedHits, refSetIndex, idxAndRecord.second.Seq); """ Suggestions? Sincerely, Brett --001a11c2caee54e68e0508306832 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Sorry to be a bother, but I decided to go back t= o the docs and start fresh and I'm still having issues. =C2=A0

We're using Qgrams, so I trying to write a simple loop= to search for all 12mers from a query sequence "seq" in the inde= x formed from a StringSet of references "refSeq", building on the= example code in the Q-Gram Index tutorial:

""&qu= ot;

=C2=A0 TFinder qgramFinder(index);

=C2=A0for (= size_t i =3D 0; i < length(seq)-12; i++)

=C2=A0{

=C2= =A0 =C2=A0 =C2=A0TInfix::Type kmer =3D infix(seq, i, i+12);

=C2= =A0 =C2=A0 =C2=A0std::cout << kmer << std::endl;

=C2=A0 =C2=A0 =C2=A0seqan::hash(indexShape(index), kmer);

<= div>=C2=A0 =C2=A0 =C2=A0for (unsigned i =3D 0; i < length(getOccurrences= (index, indexShape(index))); ++i)

=C2=A0 =C2=A0 =C2=A0{

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0std::cout << getOccurrences(index,= indexShape(index))[i] << std::endl;

=C2=A0 =C2=A0 =C2=A0}<= /div>

=C2=A0 =C2=A0 =C2=A0std::cout << std::endl;

= =C2=A0}

"""

but I&#= 39;m getting a fairly obtuse error message I don't quite understand, an= d doesn't point me back to any specific lines in my code.

"""

/usr/include/seqan/index/shape_base.h:53= 5:55: error: indirection requires pointer operand ('seqan::Segment<c= onst seqan::String<seqan::SimpleType<unsigned

=C2=A0 =C2=A0= =C2=A0 char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::Infix= Segment>' invalid)

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 hash * ValueSize<TValue>= ;::VALUE + ordValue((TValue)*it),

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0^~~

/usr/include/seqan/index/shape_base.h:548:22: no= te: in instantiation of function template specialization 'seqan::_hashF= ixedShape<unsigned long,

=C2=A0 =C2=A0 =C2=A0 seqan::SimpleTyp= e<unsigned char, seqan::Dna5_>, seqan::Segment<const seqan::String= <seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<v= oid> >,

=C2=A0 =C2=A0 =C2=A0 seqan::InfixSegment>, 12>= ;' requested here

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 return me.hValue =3D _hashFixedShape(me.hValue, it, TValue(),= UngappedShape<q>());

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0^

/home/bbowman/git/SRSLI/src/C++/SparseAlignmen= t.hpp:102:16: note: in instantiation of function template specialization &#= 39;seqan::hash<seqan::SimpleType<unsigned

=C2=A0 =C2=A0 =C2= =A0 char, seqan::Dna5_>, 12, seqan::Segment<const seqan::String<se= qan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void>= ; >, seqan::InfixSegment>

=C2=A0 =C2=A0 =C2=A0 >' re= quested here

=C2=A0 =C2=A0 =C2=A0 =C2=A0 seqan::hash(indexShape(i= ndex), kmer);

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0^

/home/bbowman/git/SRSLI/src/C++/main.cpp:86:9: note: in i= nstantiation of function template specialization 'FindSeeds2<FindSee= dsConfig<12,

=C2=A0 =C2=A0 =C2=A0 seqan::UngappedShape<12&g= t;, seqan::IndexQGram<seqan::UngappedShape<12>, seqan::Tag<seqa= n::Default_> > > >' requested here

=C2=A0 =C2=A0 = =C2=A0 =C2=A0 FindSeeds2(querySeedHits, refSetIndex, idxAndRecord.second.Se= q);

"""

Suggestions= ?

Sincerely,

Brett

--001a11c2caee54e68e0508306832-- From rene.maerker@fu-berlin.de Wed Nov 19 13:25:25 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Xr4K2-0021kJ-UZ>; Wed, 19 Nov 2014 13:25:23 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Xr4K2-0003TK-T0>; Wed, 19 Nov 2014 13:25:22 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1Xr4K2-002i0y-FQ>; Wed, 19 Nov 2014 13:25:22 +0100 Received: from EX03A.campus.fu-berlin.de ([130.133.170.134]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0210.002; Wed, 19 Nov 2014 13:25:21 +0100 From: =?utf-8?B?UmFobiwgUmVuw6k=?= To: SeqAn Development Thread-Topic: [Seqan-dev] Trouble Hashing Kmers into Qgram Index Thread-Index: AQHQA8LxrtQywv1XQ0mnyKMTKWyw7pxnz3mA Message-ID: References: In-Reply-To: Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_C870191C64024F709E64DF42EC0D38ADzedatfuberlinde_" MIME-Version: 1.0 Date: Wed, 19 Nov 2014 13:25:20 +0100 X-Original-Date: Wed, 19 Nov 2014 12:25:20 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416399922-00067E64-CE17078F/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.330353, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.4.0 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Trouble Hashing Kmers into Qgram Index X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 19 Nov 2014 12:25:25 -0000 --_000_C870191C64024F709E64DF42EC0D38ADzedatfuberlinde_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SGV5LA0KDQp0aGUgcHJvYmxlbSBsaWVzIGluIHRoZSBoYXNoKGluZGV4U2hhcGUoaW5kZXgpLCBr bWVyKSBmdW5jdGlvbi4NClRoZSBoYXNoIGZ1bmN0aW9uIG9ubHkgdGFrZXMgYW4gaXRlcmF0b3Ig b3IgcG9pbnRlciBhcyBzZWNvbmQgYXJndW1lbnQuDQpTbyBpbiB5b3VyIGNhc2UgdGhlIHNpbXBs ZSBzb2x1dGlvbiB3b3VsZCBiZSB0byBjYWxsIHRoZSBmdW5jdGlvbiBoYXNoKGluZGV4U2hhcGUo aW5kZXgpLCBpdCksIHdoaWxlIHVzaW5nIGFuIGl0ZXJhdG9yIHRvIGl0ZXJhdGUgb3ZlciB0aGUg dGV4dCBpbnN0ZWFkIG9mIHVzaW5nIHRoZSB1bnNpZ25lZCBpbnRlZ2VyLiBUaGlzIGxpdHRsZSBi ZWhhdmlvdXIgZG9lcyBub3Qgc2VlbSBvYnZpb3VzLCBhcyBpbiB0aGUgdHV0b3JpYWwgeW91IHBh c3MgYSBzdHJpbmcgbGl0ZXJhbC4gQnV0IGluIGZhY3QgYSBzdHJpbmcgbGl0ZXJhbCBpcyBqdXN0 IGEgY29uc3QgY2hhciAqLCBzbyBpdCB3b3Jrcy4NCg0KSGVyZSB5b3Ugc2VlIGFuIGV4YW1wbGUg 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relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XrPX9-0027DR-WC>; Thu, 20 Nov 2014 12:04:20 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XrPX9-0011yS-Mj>; Thu, 20 Nov 2014 12:04:19 +0100 Received: from EX03A.campus.fu-berlin.de ([130.133.170.134]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0210.002; Thu, 20 Nov 2014 12:04:18 +0100 From: "Trappe, Kathrin" To: SeqAn Development Thread-Topic: [Seqan-dev] [seqan-1.4.2] breakpoint_calculator errors Thread-Index: AQHQAeJgb2fQPqKP+Eup7ICbPb1kc5xpXlLT Message-ID: References: <546913C0.3060606@gmail.com> In-Reply-To: <546913C0.3060606@gmail.com> Accept-Language: en-GB, de-DE, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Thu, 20 Nov 2014 12:04:17 +0100 X-Original-Date: Thu, 20 Nov 2014 11:04:17 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: X X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416481460-00067E64-88CEBB25/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.4.0 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] [seqan-1.4.2] breakpoint_calculator errors X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 20 Nov 2014 11:04:22 -0000 Hi Antonio,=0A= =0A= the errors look like namespace or path errors with the Lemon library and ST= L, did you check that the Lemon lib is correctly installed and the path in = the build command is correct?=0A= =0A= cheers,=0A= Kathrin=0A= ________________________________________=0A= From: Antonio Trande [anto.trande@gmail.com]=0A= Sent: 16 November 2014 22:14=0A= To: seqan-dev@lists.fu-berlin.de=0A= Subject: [Seqan-dev] [seqan-1.4.2] breakpoint_calculator errors=0A= =0A= -----BEGIN PGP SIGNED MESSAGE-----=0A= Hash: SHA1=0A= =0A= Hi all.=0A= =0A= I need your help with these errors during SeqAn compilation on Fedora 21.= =0A= Here the full log:=0A= https://kojipkgs.fedoraproject.org//work/tasks/2027/8162027/build.log=0A= =0A= - --=0A= Antonio Trande=0A= =0A= mailto: sagitter 'at' fedoraproject 'dot' org=0A= http://fedoraos.wordpress.com/=0A= https://fedoraproject.org/wiki/User:Sagitter=0A= GPG Key: 0x66E15D00=0A= Check on https://keys.fedoraproject.org/=0A= -----BEGIN PGP SIGNATURE-----=0A= Version: GnuPG v1=0A= =0A= iQIcBAEBAgAGBQJUaRPAAAoJEFyovWBm4V0A3+cQAJJQgQuBXdj9hsH0PKcuZ+r3=0A= EyrZK0OoUdVJvtF1TUUpDPnJHVL1ZbvJN0ks4C2hGT0McMMKTy+zXHdIYlGqliXW=0A= Lxhl0pJFTQwFj2p7xnbY7D+31vBOfCLqaClId9ZLwij7sUu0zYsD8d7up99JkmrE=0A= TmblYcJmE8lechG6dmz7tW25gobcdY+Y7M7e435aCrLDHrntkE3H1YtXJOB5l11y=0A= 4otH4hd0Vo4bap//NvOZKtDSoyC46WS2ZAEOKghNwzOjdETDbubWsdsDwqK5Td98=0A= DUfFTjCFk/AoGLxeoBCGzpVDDqr5zrbXCAaOvXwbXp8D97c3tYCnjqII9l/i570k=0A= oYdJTCmvZFbx5YkG+u2pLq5DBmtC0ikQC+/f0bBlwAsoEoN8OymcIIyw+fjPLJ4t=0A= gMXzqJcKCci5pAqevKDrz49lvAfeWLg52Ud7eQUpwe6eWcDA08gvggphboAzsiMS=0A= GNkxEhvQKW1Tk5KkuRLz+VeuNOC8JNPRNDHiKNHA76wdtb+NJPQlvr2/3Qz87g+i=0A= zIkO4Svz/pzltc/RUwIQaDQxRe5Cadfnv5NWKOWA5iZ3xYBJqU8t7+um79XyY4sb=0A= 3NoZ9z/vBkmm8J5FOtsLusdWzGo0UcX0j1OAmd6mqmh//bJZ1Bb0WhgTjgERMr83=0A= VOKNsl2dzVuYbvofCIQs=0A= =3DngAX=0A= -----END PGP SIGNATURE-----=0A= =0A= _______________________________________________=0A= seqan-dev mailing list=0A= seqan-dev@lists.fu-berlin.de=0A= https://lists.fu-berlin.de/listinfo/seqan-dev=0A= From anto.trande@gmail.com Thu Nov 20 22:41:14 2014 Received: from 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against a wrong path. SeqAn code already points to private lemon sub-directory. - -- Antonio Trande mailto: sagitter 'at' fedoraproject 'dot' org http://fedoraos.wordpress.com/ https://fedoraproject.org/wiki/User:Sagitter GPG Key: 0x66E15D00 Check on https://keys.fedoraproject.org/ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBAgAGBQJUbl/ZAAoJEFyovWBm4V0ABTQP/1qWnlsfOv4RC22AgQbNqmxB OIA9V7Shq5/WekZ4CGNDFD/PnR3VPhbBqi7fEe6qQq2ILtwm4o/qI3EgrlJqkgLa zusDxdsyQhIm+1SrAAFhmvIP0g9wp4ByV47xID9fEKXe8JucV6DjTu0AHUMJzb8Z mmVGXRnfJyWMbSHj0YQnnO0Be7kBXSQnmrzLbQtUiAdWD69Y/V11xKIoUAf36KSK ZFi/zhWUmxATcuKIfcvypWoWD0+kv0W8trVuWhHbApuWRe1k4LY43+Zdba2a5F/5 gJfA+gIa13tvSwC5Xpf+SvjRLd+HLVACK+V2op7t08oxr/2GZDSgyfSyhYEFGvqJ D3VVLl3pGESb33QmHXAm6RnLAliY+5DT36ZiWLaxmKMJbi67MjraUqX58zXpJFZN PDhnzFPrKVfE5DFpVc+CvtJZSY7CpN4fL4suedi7bhyISkUE80keru2RxmK/nmEc 86K1Mqy+nYeZ0M+gy+RCcQsz9OYFNoq4S7ETkWu33B7y819MoAljphd1YUPHqxBs zN50s9GPSzpe+ucEWKdK+jAjYf2laC8EuRDmkZNLid9FTG6giOEyG3IoQOeKUx5h 5ZjKoRmFAL6kVkOdUycli/OI2VFK8V+KwEvV/mL2eqEKH8mrBvMVut1d3x+doxDL cM78MBZH4GbVnguMITtQ =qJPl -----END PGP SIGNATURE----- From bnbowman@gmail.com Fri Nov 21 02:05:13 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Xrceo-0005vK-QA>; Fri, 21 Nov 2014 02:05:06 +0100 Received: from mail-yh0-f48.google.com ([209.85.213.48]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1Xrceo-000nmQ-Fm>; Fri, 21 Nov 2014 02:05:06 +0100 Received: by mail-yh0-f48.google.com with SMTP id i57so1896031yha.21 for ; Thu, 20 Nov 2014 17:05:04 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=ZGUmeDgjgDeiynn8TZRyoNZdMGpWSJ/GOkIS+CX+SQ8=; b=XD2Upx0JUTaFsjzuokHK60mhSqlMETX6uiySI0KQch2XU7IVLMpnqI8/g4ITd32stB cb9lVdmFMJ9t4zzuAofL6GzmrXnTYuWR+8hcHg6Px1S6l04obCifFXRMIXdXRw0Bo1/O UhWspg51rV0puhTPWqo9eRxyUl/t9C1vJRF4KFj+VRdDnro5BOQrPzvE099rtimDYBH7 8RoU6QCDzUzFT5X10jpNc8wNs5vLVAeUe/yXZ35yiJv/5caOIcpYwPsG2Qw2FY1HWyCm DAwQ6qBir1IdhwCnLr8pXHW1w4xRwdythqQjDQmfo5pJcbWS8Z+1xaGl8g5+teILtOvN FI/g== MIME-Version: 1.0 X-Received: by 10.170.36.133 with SMTP id 127mr33104yke.109.1416531903841; Thu, 20 Nov 2014 17:05:03 -0800 (PST) Received: by 10.170.110.19 with HTTP; Thu, 20 Nov 2014 17:05:03 -0800 (PST) In-Reply-To: References:

Date: Thu, 20 Nov 2014 17:05:03 -0800 Message-ID: From: Brett Bowman To: SeqAn Development Content-Type: multipart/alternative; boundary=001a1137c7d6f12937050854080d X-Originating-IP: 209.85.213.48 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416531906-00067E64-B839BF78/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.498806, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.4.0 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Trouble Hashing Kmers into Qgram Index X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 21 Nov 2014 01:05:13 -0000 --001a1137c7d6f12937050854080d Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks Rene, those solutions worked for me. I have two follow-up Qgram Index questions: 1) Is there any way to iterate over all of the Kmers stored in a Qgram index? You have sample code for the other index types here ( http://seqan.readthedocs.org/en/master/Tutorial/IndexIterators.html), but it doesn't seem to work for me for the QgramIndx: """ typedef Iterator>> TIter; TIter::Type it(refSetIndex); do { // Print theletters from the root to the current node std::cout << representative(it) << std::endl; if (!goDown(it) && !goRight(it)) while (goUp(it) && !goRight(it)); } while (!isRoot(it)); '""" 2) Is there any way to mask or remove certain Kmers from an Index once it's been created? I.e., to hide or delete common, low-complexity Kmers like homopolymers -Brett On Wed, Nov 19, 2014 at 4:25 AM, Rahn, Ren=C3=A9 wrote: > Hey, > > the problem lies in the hash(indexShape(index), kmer) function. > The hash function only takes an iterator or pointer as second argument. > So in your case the simple solution would be to call the function > hash(indexShape(index), it), while using an iterator to iterate over the > text instead of using the unsigned integer. This little behaviour does no= t > seem obvious, as in the tutorial you pass a string literal. But in fact a > string literal is just a const char *, so it works. > > Here you see an example code to work with a) using the finder interface > and b) directly operating on the index. > IHTH. > > cheers, > > Ren=C3=A9 > > typedef Index > > > TQGramIndex; > typedef Finder TFinder; > typedef Iterator::Type TIterator; > typedef Fibre::Type TShape; > > TQGramIndex index(ref); > indexRequire(index, QGramSADir()); // On-demand index creation. > > // a) Using the finder interface. > TFinder finder(index); > > for (TIterator it =3D begin(query, Standard()); it !=3D end(query, > Standard()) - 12; ++it) > { > std::cout << "Occ at: "; > while(find(finder, infix(query, it, it+12))) > std::cout << position(finder) << " "; > std::cout << std::endl; > clear(finder); // Clear finder for next search. > } > > // b) Using the index interface. > TShape & shape =3D indexShape(index); > hashInit(shape, begin(query, Standard())); > for (TIterator it =3D begin(query, Standard()); it !=3D end(query, > Standard()) - 12; ++it) > { > std::cout << "Occ at: "; > hashNext(shape, it); > for (unsigned i =3D 0; i < length(getOccurrences(index, shape)); > ++i) > std::cout << getOccurrences(index, shape)[i] << " "; > std::cout << std::endl; > > } > > On 19 Nov 2014, at 07:34, Brett Bowman wrote: > > Sorry to be a bother, but I decided to go back to the docs and start > fresh and I'm still having issues. > > We're using Qgrams, so I trying to write a simple loop to search for all > 12mers from a query sequence "seq" in the index formed from a StringSet o= f > references "refSeq", building on the example code in the Q-Gram Index > tutorial: > """ > TFinder qgramFinder(index); > for (size_t i =3D 0; i < length(seq)-12; i++) > { > TInfix::Type kmer =3D infix(seq, i, i+12); > std::cout << kmer << std::endl; > > seqan::hash(indexShape(index), kmer); > for (unsigned i =3D 0; i < length(getOccurrences(index, > indexShape(index))); ++i) > { > std::cout << getOccurrences(index, indexShape(index))[i] << > std::endl; > } > std::cout << std::endl; > } > """ > > but I'm getting a fairly obtuse error message I don't quite understand, > and doesn't point me back to any specific lines in my code. > > """ > /usr/include/seqan/index/shape_base.h:535:55: error: indirection requires > pointer operand ('seqan::Segment seqan::String char, seqan::Dna5_>, seqan::Alloc >, seqan::InfixSegment>' > invalid) > hash * ValueSize::VALUE + > ordValue((TValue)*it), > > ^~~ > /usr/include/seqan/index/shape_base.h:548:22: note: in instantiation of > function template specialization 'seqan::_hashFixedShape seqan::SimpleType, seqan::Segment seqan::String, > seqan::Alloc >, > seqan::InfixSegment>, 12>' requested here > return me.hValue =3D _hashFixedShape(me.hValue, it, > TValue(), UngappedShape()); > ^ > /home/bbowman/git/SRSLI/src/C++/SparseAlignment.hpp:102:16: note: in > instantiation of function template specialization > 'seqan::hash char, seqan::Dna5_>, 12, seqan::Segment seqan::String, > seqan::Alloc >, seqan::InfixSegment> > >' requested here > seqan::hash(indexShape(index), kmer); > ^ > /home/bbowman/git/SRSLI/src/C++/main.cpp:86:9: note: in instantiation of > function template specialization 'FindSeeds2 seqan::UngappedShape<12>, > seqan::IndexQGram, seqan::Tag >= > > >' requested here > FindSeeds2(querySeedHits, refSetIndex, idxAndRecord.second.Seq); > """ > > Suggestions? > > Sincerely, > Brett > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > > --- > > Ren=C3=A9 Rahn > Ph.D. Student > -------------------------------- > Tel: (+49) 30 838 75277 > Mail: rene.rahn@fu-berlin.de > -------------------------------- > Institute of Computer Science > Algorithmic Bioinformatics (ABI) > -------------------------------- > Freie Universit=C3=A4t Berlin > Takustra=C3=9Fe 9 > 14195 Berlin > -------------------------------- > > > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev > > --001a1137c7d6f12937050854080d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Thanks Rene, those solutions worked for me.

I have two follow-up Qgram Index questions:

1= ) Is there any way to iterate over all of the Kmers stored in a Qgram index= ?=C2=A0 You have sample code for the other index types here (http://se= qan.readthedocs.org/en/master/Tutorial/IndexIterators.html), but it doe= sn't seem to work for me for the QgramIndx:

"""= ;

=C2=A0typedef Iterator<TIndex, TopDown<ParentLinks&l= t;>>> TIter;

=C2=A0TIter::Type it(refSetI= ndex);

=C2=A0do {

=C2=A0 =C2=A0 =C2=A0// Print thelette= rs from the root to the current node

=C2=A0 =C2=A0 =C2=A0std::cou= t << representative(it) << std::endl;

= =C2=A0 =C2=A0 =C2=A0if (!goDown(it) && !goRight(it))

=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0while (goUp(it) && !goRight(it));

=C2=A0} while (!isRoot(it));

'"""= ;

2) Is there any way to mask or remove certain Km= ers from an Index once it's been created?=C2=A0 I.e., to hide or delete= common, low-complexity Kmers like homopolymers

-B= rett

On Wed, Nov 19, 2014 at 4:25 AM= , Rahn, Ren=C3=A9 <rene.maerker@fu-berlin.de> wrote:=

Hey,

the problem lies in the hash(indexShape(index), kmer) function.

The hash function only takes an iterator or pointer as second argument= .=C2=A0

So in your case the simple solution would be to call the function hash= (indexShape(index), it), while using an iterator to iterate over the text i= nstead of using the unsigned integer. This little behaviour does not seem o= bvious, as in the tutorial you pass a string literal. But in fact a string literal is just a const ch= ar *, so it works.

Here you see an example code to work with a) using the finder interfac= e and b) directly operating on the index.

IHTH.

cheers,

Ren=C3=A9=C2=A0

=C2=A0 =C2=A0=C2=A0typedef Index<DnaString, IndexQGram<UngappedShape<12> > > TQGramIndex;

=C2=A0 =C2=A0 typedef Finder<TQGramIndex> TFinder;

=C2=A0 =C2=A0 typedef Iterator<DnaString, Standard>::Type TIterator;

=C2=A0 =C2=A0 typedef Fibre<TQGramIndex, QGramShape>::Type TShape;

=C2=A0 =C2=A0 TQGramIndex index(ref);

=C2=A0 =C2=A0 indexRequire(index, QGramSADir());=C2=A0 // On-demand index creation.

=C2=A0 =C2=A0 // a) Using the finder interface.

=C2=A0 =C2=A0 TFinder finder(index);

=C2=A0 =C2=A0 for (TIterator it =3D begin(query, Standard()); it !=3D end(query, Standard()) - 12; ++it)

=C2=A0 =C2=A0 {

=C2=A0 =C2=A0 =C2=A0 =C2=A0 std::cout << "Occ at: ";

=C2=A0 =C2=A0 =C2=A0 =C2=A0 whi= le(find(finder, infix(query, it, it+12)))

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 std::cout << position(finder) << " ";

=C2=A0 =C2=A0 =C2=A0 =C2=A0 std::cout << std::endl;

=C2=A0 =C2=A0 =C2=A0 =C2=A0 clear(finder);=C2=A0 // Clear finder for next search.

=C2=A0 =C2=A0 }

=C2=A0 =C2=A0 // b) Using the index interface.

=C2=A0 =C2=A0 TShape & shape =3D indexShape(index);

=C2=A0 =C2=A0 hashInit(shape, begin(query, Standard()));

=C2=A0 =C2=A0 for (TIterator it =3D begin(query, Standard()); it !=3D end(query, Standard()) - 12; ++it)

=C2=A0 =C2=A0 {

=C2=A0 =C2=A0 =C2=A0 =C2=A0 std::cout << "Occ at: ";

=C2=A0 =C2=A0 =C2=A0 =C2=A0 hashNext(shape, it);

=C2=A0 =C2=A0 =C2=A0 =C2=A0 for= (unsigned i =3D 0; i < length(getOccurrences(index, sh= ape)); ++i)

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 std::cout << getOccurrences(index, shape)[i]= << " ";

=C2=A0 =C2=A0 =C2=A0 =C2=A0 std::cout << std::endl;

=C2=A0 =C2=A0 }

On 19 Nov 2014, at 07:34, Brett Bowman <bnbowman@gmail.com> wrote:

Sorry to be a bother, but I decided to go back to the docs and start f= resh and I'm still having issues. =C2=A0

We're using Qgrams, so I trying to write a simple loop to search f= or all 12mers from a query sequence "seq" in the index formed fro= m a StringSet of references "refSeq", building on the example cod= e in the Q-Gram Index tutorial:

"""

=C2=A0 TFinder qgramFinder(index);

=C2=A0for (size_t i =3D 0; i < length(seq)-12; i++)

=C2=A0{

=C2=A0 =C2=A0 =C2=A0TInfix::Type kmer =3D infix(seq, i, i+12);

=C2=A0 =C2=A0 =C2=A0std::cout << kmer << std::endl;

=C2=A0 =C2=A0 =C2=A0seqan::hash(indexShape(index), kmer);

=C2=A0 =C2=A0 =C2=A0for (unsigned i =3D 0; i < length(getOccurrence= s(index, indexShape(index))); ++i)

=C2=A0 =C2=A0 =C2=A0{

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0std::cout << getOccurrences(in= dex, indexShape(index))[i] << std::endl;

=C2=A0 =C2=A0 =C2=A0}

=C2=A0 =C2=A0 =C2=A0std::cout << std::endl;

=C2=A0}

"""

but I'm getting a fairly obtuse error message I don't quite un= derstand, and doesn't point me back to any specific lines in my code.

"""

/usr/include/seqan/index/shape_base.h:535:55: error: indirection requi= res pointer operand ('seqan::Segment<const seqan::String<seqan::S= impleType<unsigned

=C2=A0 =C2=A0 =C2=A0 char, seqan::Dna5_>, seqan::Alloc<void> = >, seqan::InfixSegment>' invalid)

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 hash * ValueSize<TValue>::VALUE + ordValue((TValue)*it)= ,

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~

/usr/include/seqan/index/shape_base.h:548:22: note: in instantiation o= f function template specialization 'seqan::_hashFixedShape<unsigned = long,

=C2=A0 =C2=A0 =C2=A0 seqan::SimpleType<unsigned char, seqan::Dna5_&= gt;, seqan::Segment<const seqan::String<seqan::SimpleType<unsigned= char, seqan::Dna5_>, seqan::Alloc<void> >,

=C2=A0 =C2=A0 =C2=A0 seqan::InfixSegment>, 12>' requested he= re

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 return me.hVal= ue =3D _hashFixedShape(me.hValue, it, TValue(), UngappedShape<q>());<= /div>
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^

/home/bbowman/git/SRSLI/src/C++/SparseAlignment.hpp:102:16: note: in i= nstantiation of function template specialization 'seqan::hash<seqan:= :SimpleType<unsigned

=C2=A0 =C2=A0 =C2=A0 char, seqan::Dna5_>, 12, seqan::Segment<con= st seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, s= eqan::Alloc<void> >, seqan::InfixSegment>

=C2=A0 =C2=A0 =C2=A0 >' requested here

=C2=A0 =C2=A0 =C2=A0 =C2=A0 seqan::hash(indexShape(index), kmer);
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^

/home/bbowman/git/SRSLI/src/C++/main.cpp:86:9: note: in instantiation = of function template specialization 'FindSeeds2<FindSeedsConfig<1= 2,

=C2=A0 =C2=A0 =C2=A0 seqan::UngappedShape<12>, seqan::IndexQGram= <seqan::UngappedShape<12>, seqan::Tag<seqan::Default_> > = > >' requested here

=C2=A0 =C2=A0 =C2=A0 =C2=A0 FindSeeds2(querySeedHits, refSetIndex, idx= AndRecord.second.Seq);

"""

Suggestions?

Sincerely,

Brett

_______________________________________________
seqan-dev mailing list
seqan-dev= @lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev

---

Ren=C3=A9 Rahn

Ph.D. Student

--------------------------------

Tel: =C2=A0(+49) 30 838 75277=

Mail:=C2=A0rene.rahn@fu-berlin.de

--------------------------------

Institute of Computer Science

Algorithmic Bioinformatics (ABI)
--------------------------------
Freie Universit=C3=A4t Berlin

Takustra=C3=9Fe 9

14195 Berlin

--------------------------------

_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.d= e
https://lists.fu-berlin.de/listinfo/seqan-dev

--001a1137c7d6f12937050854080d-- From ctb@msu.edu Fri Nov 21 15:44:51 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XrpS5-002IFR-RF>; Fri, 21 Nov 2014 15:44:49 +0100 Received: from teckla.idyll.org ([69.55.232.123]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XrpS5-003pKD-L0>; Fri, 21 Nov 2014 15:44:49 +0100 Received: from [35.10.138.45] (helo=[10.0.1.78]) by teckla.idyll.org with esmtpa (Exim 4.69) (envelope-from ) id 1XrpS3-0000vK-28; Fri, 21 Nov 2014 06:44:47 -0800 Mime-Version: 1.0 (Mac OS X Mail 7.3 $1878.6$) Content-Type: text/plain; charset=windows-1252 From: "C. Titus Brown" Resent-Cc: "Michael R. Crusoe" Resent-From: "C. Titus Brown" Date: Fri, 21 Nov 2014 09:38:57 -0500 Content-Transfer-Encoding: quoted-printable Resent-Date: Fri, 21 Nov 2014 09:44:45 -0500 Message-Id: <170A0CA2-59F1-41A7-A998-317B81059EF0@msu.edu> Resent-To: seqan-dev@lists.fu-berlin.de To: seqan-dev@lists.fu-berlin.de X-Mailer: Apple Mail (2.1878.6) Resent-Message-Id: X-Originating-IP: 69.55.232.123 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416581089-00067E64-8453D2F4/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.200672, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=none X-Spam-Checker-Version: SpamAssassin 3.4.0 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Cc: "Michael R. Crusoe" Subject: [Seqan-dev] Hello from the khmer project! X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 21 Nov 2014 14:44:52 -0000 Dear SeqAn, just a brief intro and heads up =97 we have a PR for the khmer project, https://github.com/ged-lab/khmer/pull/642 that switches over to using SeqAn for our sequencing parsing. It will = most likely be merged for the next major release, v1.2 If you=92re unfamiliar with khmer, here=92s an intro paper: = http://files.figshare.com/1194736/wssspe13_ged.pdf At some point we hope to be chatting with you more closely about issues = that include streaming support and threading. In the meantime please = rely on us for any letters of support or collaboration that you can use! I=92m the PI on the main khmer grant, and Michael Crusoe, CCed, is the = lead khmer developer and community liaison. best, =97titus ----------------------------- Dr. C. Titus Brown, ctbrown@ucdavis.edu Visiting Associate Prof., UC Davis http://ged.msu.edu/= From t@teckla.idyll.org Fri Nov 21 15:45:33 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XrpSl-002IT2-1c>; Fri, 21 Nov 2014 15:45:31 +0100 Received: from teckla.idyll.org ([69.55.232.123]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XrpSk-003pWa-Rb>; Fri, 21 Nov 2014 15:45:31 +0100 Received: from t by teckla.idyll.org with local (Exim 4.69) (envelope-from ) id 1XrpSi-00011E-Aj; Fri, 21 Nov 2014 06:45:28 -0800 Date: Fri, 21 Nov 2014 06:45:28 -0800 From: "C. Titus Brown" To: seqan-dev@lists.fu-berlin.de Message-ID: <20141121144528.GB32133@idyll.org> References: <170A0CA2-59F1-41A7-A998-317B81059EF0@msu.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <170A0CA2-59F1-41A7-A998-317B81059EF0@msu.edu> User-Agent: Mutt/1.5.18 (2008-05-17) X-Originating-IP: 69.55.232.123 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416581131-00067E64-66CDDB8E/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.101836, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=none X-Spam-Checker-Version: SpamAssassin 3.4.0 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Cc: "Michael R. Crusoe" Subject: Re: [Seqan-dev] Hello from the khmer project! X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: titus@idyll.org, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Nov 2014 14:45:33 -0000 And, uhh, p.s. -- thanks for all the work on SeqAn! :) Sorry, forgot to say that! cheers, --titus On Fri, Nov 21, 2014 at 09:38:57AM -0500, C. Titus Brown wrote: > Dear SeqAn, > > just a brief intro and heads up ? we have a PR for the khmer project, > > https://github.com/ged-lab/khmer/pull/642 > > that switches over to using SeqAn for our sequencing parsing. It will most likely be merged for the next major release, v1.2 > > If you?re unfamiliar with khmer, here?s an intro paper: http://files.figshare.com/1194736/wssspe13_ged.pdf > > At some point we hope to be chatting with you more closely about issues that include streaming support and threading. In the meantime please rely on us for any letters of support or collaboration that you can use! > > I?m the PI on the main khmer grant, and Michael Crusoe, CCed, is the lead khmer developer and community liaison. > > best, > ?titus > ----------------------------- > > Dr. C. Titus Brown, ctbrown@ucdavis.edu > Visiting Associate Prof., UC Davis > http://ged.msu.edu/ > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev -- C. Titus Brown, ctb@msu.edu From Knut.Reinert@fu-berlin.de Fri Nov 21 16:03:52 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XrpkU-002LnD-07>; Fri, 21 Nov 2014 16:03:50 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XrpkT-001IY8-VG>; Fri, 21 Nov 2014 16:03:49 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XrpkT-003ydy-Lk>; Fri, 21 Nov 2014 16:03:49 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0210.002; Fri, 21 Nov 2014 16:03:48 +0100 From: "Reinert, Knut" To: SeqAn Development Thread-Topic: [Seqan-dev] Hello from the khmer project! Thread-Index: AQHQBZnBftEbCLi/NU6ywmwOhgh+LZxrLYB8 Message-ID: <74669129-2479-4361-9A55-2E4BC7AD73E1@fu-berlin.de> References: <170A0CA2-59F1-41A7-A998-317B81059EF0@msu.edu> In-Reply-To: <170A0CA2-59F1-41A7-A998-317B81059EF0@msu.edu> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Fri, 21 Nov 2014 16:03:46 +0100 X-Original-Date: Fri, 21 Nov 2014 15:03:46 +0000 X-Originating-IP: 130.133.170.202 X-ZEDAT-Hint: X X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1416582230-00067E64-839B4008/2/15101991804 X-Bogosity: Ham, tests=bogofilter, spamicity=0.149611, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-49.0 required=5.0 tests=ALL_TRUSTED, FU_XPURGATE_SUSP X-Spam-Checker-Version: SpamAssassin 3.4.0 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Hello from the khmer project! X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 21 Nov 2014 15:03:52 -0000 Hi Titus, Thanks for the update! We are currently in a transition phase of some personnel and will release s= eqAn 2.0 this year. In spring we will do a Renault of our website and plan to include more I fo= r about partners and users of SeqAn. So if it is the ok I will approach you then for more details? All the best, Knut Sent from my iPad, sorry for being short. > On Nov 21, 2014, at 15:45, C. Titus Brown wrote: >=20 > Dear SeqAn, >=20 > just a brief intro and heads up =97 we have a PR for the khmer project, >=20 > https://github.com/ged-lab/khmer/pull/642 >=20 > that switches over to using SeqAn for our sequencing parsing. It will mo= st likely be merged for the next major release, v1.2 >=20 > If you=92re unfamiliar with khmer, here=92s an intro paper: http://files.= figshare.com/1194736/wssspe13_ged.pdf >=20 > At some point we hope to be chatting with you more closely about issues t= hat include streaming support and threading. In the meantime please rely o= n us for any letters of support or collaboration that you can use! >=20 > I=92m the PI on the main khmer grant, and Michael Crusoe, CCed, is the le= ad khmer developer and community liaison. >=20 > best, > =97titus > ----------------------------- >=20 > Dr. C. Titus Brown, ctbrown@ucdavis.edu > Visiting Associate Prof., UC Davis > http://ged.msu.edu/ > _______________________________________________ > seqan-dev mailing list > seqan-dev@lists.fu-berlin.de > https://lists.fu-berlin.de/listinfo/seqan-dev From t@teckla.idyll.org Fri Nov 21 16:08:59 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XrppR-002MXv-1s>; Fri, 21 Nov 2014 16:08:57 +0100 Received: from teckla.idyll.org ([69.55.232.123]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XrppQ-003wDw-RR>; Fri, 21 Nov 2014 16:08:57 +0100 Received: from t by teckla.idyll.org with local (Exim 4.69) (envelope-from ) id 1XrppO-00068B-2o; Fri, 21 Nov 2014 07:08:54 -0800 Date: Fri, 21 Nov 2014 07:08:54 -0800 From: "C. Titus Brown" To: SeqAn Development Message-ID: <20141121150854.GC32133@idyll.org> References: <170A0CA2-59F1-41A7-A998-317B81059EF0@msu.edu> <74669129-2479-4361-9A55-2E4BC7AD73E1@fu-berlin.de> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <74669129-2479-4361-9A55-2E4BC7AD73E1@fu-berlin.de> User-Agent: Mutt/1.5.18 (2008-05-17) X-Originating-IP: 69.55.232.123 X-purgate: suspect X-purgate-type: suspect X-purgate-ID: 151147::1416582537-00067E64-A2051711/2/15101991804 X-Bogosity: Ham, tests=bogofilter, spamicity=0.020636, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=1.0 required=5.0 tests=FU_XPURGATE_SUSP X-Spam-Checker-Version: SpamAssassin 3.4.0 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: x Cc: mcrusoe@msu.edu Subject: Re: [Seqan-dev] Hello from the khmer project! X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: titus@idyll.org, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Nov 2014 15:08:59 -0000 On Fri, Nov 21, 2014 at 04:03:46PM +0100, Reinert, Knut wrote: > Hi Titus, > > Thanks for the update! > > We are currently in a transition phase of some personnel and will release seqAn 2.0 this year. > In spring we will do a Renault of our website and plan to include more I for about partners and users of SeqAn. > > So if it is the ok I will approach you then for more details? Sounds good! best, --titus > Sent from my iPad, sorry for being short. > > > On Nov 21, 2014, at 15:45, C. Titus Brown wrote: > > > > Dear SeqAn, > > > > just a brief intro and heads up ? we have a PR for the khmer project, > > > > https://github.com/ged-lab/khmer/pull/642 > > > > that switches over to using SeqAn for our sequencing parsing. It will most likely be merged for the next major release, v1.2 > > > > If you?re unfamiliar with khmer, here?s an intro paper: http://files.figshare.com/1194736/wssspe13_ged.pdf > > > > At some point we hope to be chatting with you more closely about issues that include streaming support and threading. In the meantime please rely on us for any letters of support or collaboration that you can use! > > > > I?m the PI on the main khmer grant, and Michael Crusoe, CCed, is the lead khmer developer and community liaison. > > > > best, > > ?titus > > ----------------------------- > > > > Dr. C. Titus Brown, ctbrown@ucdavis.edu > > Visiting Associate Prof., UC Davis > > http://ged.msu.edu/ > > _______________________________________________ > > 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 -- C. Titus Brown, ctb@msu.edu From theo@stillwater-sc.com Sat Nov 22 16:18:00 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XsCRi-0005OQ-6r>; Sat, 22 Nov 2014 16:17:58 +0100 Received: from mail12c40.carrierzone.com ([209.235.156.152]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XsCRh-0042F7-K3>; Sat, 22 Nov 2014 16:17:58 +0100 X-Authenticated-User: theo.stillwater-sc.com Received: from [192.168.1.119] (173-162-153-241-NewEngland.hfc.comcastbusiness.net [173.162.153.241]) (authenticated bits=0) by mail12c40.carrierzone.com (8.13.6/8.13.1) with ESMTP id sAMFHoAQ006871 for ; Sat, 22 Nov 2014 15:17:52 +0000 Message-ID: <5470A923.5080202@stillwater-sc.com> Date: Sat, 22 Nov 2014 10:17:55 -0500 From: Theodore Omtzigt Organization: Stillwater Supercomputing, Inc. User-Agent: Mozilla/5.0 (Windows NT 6.3; WOW64; rv:24.0) Gecko/20100101 Thunderbird/24.6.0 MIME-Version: 1.0 To: seqan-dev@lists.fu-berlin.de References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable X-CTCH-RefID: str=0001.0A020203.5470A920.0210, ss=1, re=0.001, recu=0.000, reip=0.000, cl=1, cld=1, fgs=0 X-CTCH-VOD: Unknown X-CTCH-Spam: Unknown X-CTCH-Score: 0.001 X-CTCH-Rules: C_4847, X-CTCH-Flags: 0 X-CTCH-ScoreCust: 0.000 X-Origin-Country: US X-Originating-IP: 209.235.156.152 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416669478-00067E64-0C6E6D04/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.350860, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=RCVD_IN_DNSWL_NONE X-Spam-Checker-Version: SpamAssassin 3.4.0 on Gabun.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 59, Issue 11 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 22 Nov 2014 15:18:01 -0000 This is fantastic! I am a big fan of Seqan and khmer and we have been trying to figure out how to hardware accelerate khmer, in particular, the digital renormalization step. Seqan's meta-programmed API is meant to abstract away the underlying 'algorithm' and is thus the perfect interface for hardware accelerated systems. This collaboration would solve the hardware acceleration dilemma of too many software packages with too many APIs and with too little structure. Hardware acceleration for genomics/proteomics has such a phenomenal upside since the core operators, small alphabets, string operators, string search, Bloom filters, hash functions, etc. are so poorly supported by general purpose CPUs and GPUs that custom hardware can easily get to 100x speedups. The biggest problem is the broad and unstructured software landscape. Seqan as a common library would go a long way to resolve the software proliferation problem. Let me know if there is anything we can help with. Theo CEO Stillwater Supercomputing, Inc. http://www.stillwater-sc.com/ =20 On 11/22/2014 6:00 AM, seqan-dev-request@lists.fu-berlin.de wrote: > Send seqan-dev mailing list submissions to > seqan-dev@lists.fu-berlin.de > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.fu-berlin.de/listinfo/seqan-dev > or, via email, send a message with subject or body 'help' to > seqan-dev-request@lists.fu-berlin.de > > You can reach the person managing the list at > seqan-dev-owner@lists.fu-berlin.de > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of seqan-dev digest..." > > > Today's Topics: > > 1. Hello from the khmer project! (C. Titus Brown) > 2. Re: Hello from the khmer project! (C. Titus Brown) > 3. Re: Hello from the khmer project! (Reinert, Knut) > 4. Re: Hello from the khmer project! (C. Titus Brown) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 21 Nov 2014 09:38:57 -0500 > From: "C. Titus Brown" > To: seqan-dev@lists.fu-berlin.de > Cc: "Michael R. Crusoe" > Subject: [Seqan-dev] Hello from the khmer project! > Message-ID: <170A0CA2-59F1-41A7-A998-317B81059EF0@msu.edu> > Content-Type: text/plain; charset=3Dwindows-1252 > > Dear SeqAn, > > just a brief intro and heads up ? we have a PR for the khmer project, > > https://github.com/ged-lab/khmer/pull/642 > > that switches over to using SeqAn for our sequencing parsing. It will = most likely be merged for the next major release, v1.2 > > If you?re unfamiliar with khmer, here?s an intro paper: http://files.fi= gshare.com/1194736/wssspe13_ged.pdf > > At some point we hope to be chatting with you more closely about issues= that include streaming support and threading. In the meantime please re= ly on us for any letters of support or collaboration that you can use! > > I?m the PI on the main khmer grant, and Michael Crusoe, CCed, is the le= ad khmer developer and community liaison. > > best, > ?titus > ----------------------------- > > Dr. C. Titus Brown, ctbrown@ucdavis.edu > Visiting Associate Prof., UC Davis > http://ged.msu.edu/ > > > ------------------------------ > > Message: 2 > Date: Fri, 21 Nov 2014 06:45:28 -0800 > From: "C. Titus Brown" > To: seqan-dev@lists.fu-berlin.de > Cc: "Michael R. Crusoe" > Subject: Re: [Seqan-dev] Hello from the khmer project! > Message-ID: <20141121144528.GB32133@idyll.org> > Content-Type: text/plain; charset=3Dus-ascii > > And, uhh, p.s. -- thanks for all the work on SeqAn! :) Sorry, forgot t= o say > that! > > cheers, > --titus > > On Fri, Nov 21, 2014 at 09:38:57AM -0500, C. Titus Brown wrote: >> Dear SeqAn, >> >> just a brief intro and heads up ? we have a PR for the khmer project, >> >> https://github.com/ged-lab/khmer/pull/642 >> >> that switches over to using SeqAn for our sequencing parsing. It will= most likely be merged for the next major release, v1.2 >> >> If you?re unfamiliar with khmer, here?s an intro paper: http://files.f= igshare.com/1194736/wssspe13_ged.pdf >> >> At some point we hope to be chatting with you more closely about issue= s that include streaming support and threading. In the meantime please r= ely on us for any letters of support or collaboration that you can use! >> >> I?m the PI on the main khmer grant, and Michael Crusoe, CCed, is the l= ead khmer developer and community liaison. >> >> best, >> ?titus >> ----------------------------- >> >> Dr. C. Titus Brown, ctbrown@ucdavis.edu >> Visiting Associate Prof., UC Davis >> http://ged.msu.edu/ >> _______________________________________________ >> seqan-dev mailing list >> seqan-dev@lists.fu-berlin.de >> https://lists.fu-berlin.de/listinfo/seqan-dev From t@teckla.idyll.org Sat Nov 22 23:19:56 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XsJ1x-000aHB-T4>; Sat, 22 Nov 2014 23:19:50 +0100 Received: from teckla.idyll.org ([69.55.232.123]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XsJ1x-0011QF-GJ>; Sat, 22 Nov 2014 23:19:49 +0100 Received: from t by teckla.idyll.org with local (Exim 4.69) (envelope-from ) id 1XsJ1t-0007n7-Oi for seqan-dev@lists.fu-berlin.de; Sat, 22 Nov 2014 14:19:45 -0800 Date: Sat, 22 Nov 2014 14:19:45 -0800 From: "C. Titus Brown" To: SeqAn Development Message-ID: <20141122221945.GI22300@idyll.org> References: <5470A923.5080202@stillwater-sc.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <5470A923.5080202@stillwater-sc.com> User-Agent: Mutt/1.5.18 (2008-05-17) X-Originating-IP: 69.55.232.123 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416694789-00067E64-F035C35A/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.163870, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=none X-Spam-Checker-Version: SpamAssassin 3.4.0 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] seqan-dev Digest, Vol 59, Issue 11 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 Precedence: list Reply-To: titus@idyll.org, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 22 Nov 2014 22:19:56 -0000 Thanks, Theo -- nothing comes to mind but we are open to patches from you, if it makes your life easier for us to maintain them. (I mean, they shouldn't be totally irrelevant and a maintenance burden, but we have no objection to adding in refactorings that you've done.) cheers, --titus On Sat, Nov 22, 2014 at 10:17:55AM -0500, Theodore Omtzigt wrote: > This is fantastic! I am a big fan of Seqan and khmer and we have been > trying to figure out how to hardware accelerate khmer, in particular, > the digital renormalization step. Seqan's meta-programmed API is meant > to abstract away the underlying 'algorithm' and is thus the perfect > interface for hardware accelerated systems. This collaboration would > solve the hardware acceleration dilemma of too many software packages > with too many APIs and with too little structure. Hardware acceleration > for genomics/proteomics has such a phenomenal upside since the core > operators, small alphabets, string operators, string search, Bloom > filters, hash functions, etc. are so poorly supported by general purpose > CPUs and GPUs that custom hardware can easily get to 100x speedups. The > biggest problem is the broad and unstructured software landscape. Seqan > as a common library would go a long way to resolve the software > proliferation problem. > > Let me know if there is anything we can help with. > > Theo > CEO > Stillwater Supercomputing, Inc. > http://www.stillwater-sc.com/ > > On 11/22/2014 6:00 AM, seqan-dev-request@lists.fu-berlin.de wrote: > > Send seqan-dev mailing list submissions to > > seqan-dev@lists.fu-berlin.de > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://lists.fu-berlin.de/listinfo/seqan-dev > > or, via email, send a message with subject or body 'help' to > > seqan-dev-request@lists.fu-berlin.de > > > > You can reach the person managing the list at > > seqan-dev-owner@lists.fu-berlin.de > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of seqan-dev digest..." > > > > > > Today's Topics: > > > > 1. Hello from the khmer project! (C. Titus Brown) > > 2. Re: Hello from the khmer project! (C. Titus Brown) > > 3. Re: Hello from the khmer project! (Reinert, Knut) > > 4. Re: Hello from the khmer project! (C. Titus Brown) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 21 Nov 2014 09:38:57 -0500 > > From: "C. Titus Brown" > > To: seqan-dev@lists.fu-berlin.de > > Cc: "Michael R. Crusoe" > > Subject: [Seqan-dev] Hello from the khmer project! > > Message-ID: <170A0CA2-59F1-41A7-A998-317B81059EF0@msu.edu> > > Content-Type: text/plain; charset=windows-1252 > > > > Dear SeqAn, > > > > just a brief intro and heads up ? we have a PR for the khmer project, > > > > https://github.com/ged-lab/khmer/pull/642 > > > > that switches over to using SeqAn for our sequencing parsing. It will most likely be merged for the next major release, v1.2 > > > > If you?re unfamiliar with khmer, here?s an intro paper: http://files.figshare.com/1194736/wssspe13_ged.pdf > > > > At some point we hope to be chatting with you more closely about issues that include streaming support and threading. In the meantime please rely on us for any letters of support or collaboration that you can use! > > > > I?m the PI on the main khmer grant, and Michael Crusoe, CCed, is the lead khmer developer and community liaison. > > > > best, > > ?titus > > ----------------------------- > > > > Dr. C. Titus Brown, ctbrown@ucdavis.edu > > Visiting Associate Prof., UC Davis > > http://ged.msu.edu/ > > > > > > ------------------------------ > > > > Message: 2 > > Date: Fri, 21 Nov 2014 06:45:28 -0800 > > From: "C. Titus Brown" > > To: seqan-dev@lists.fu-berlin.de > > Cc: "Michael R. Crusoe" > > Subject: Re: [Seqan-dev] Hello from the khmer project! > > Message-ID: <20141121144528.GB32133@idyll.org> > > Content-Type: text/plain; charset=us-ascii > > > > And, uhh, p.s. -- thanks for all the work on SeqAn! :) Sorry, forgot to say > > that! > > > > cheers, > > --titus > > > > On Fri, Nov 21, 2014 at 09:38:57AM -0500, C. Titus Brown wrote: > >> Dear SeqAn, > >> > >> just a brief intro and heads up ? we have a PR for the khmer project, > >> > >> https://github.com/ged-lab/khmer/pull/642 > >> > >> that switches over to using SeqAn for our sequencing parsing. It will most likely be merged for the next major release, v1.2 > >> > >> If you?re unfamiliar with khmer, here?s an intro paper: http://files.figshare.com/1194736/wssspe13_ged.pdf > >> > >> At some point we hope to be chatting with you more closely about issues that include streaming support and threading. In the meantime please rely on us for any letters of support or collaboration that you can use! > >> > >> I?m the PI on the main khmer grant, and Michael Crusoe, CCed, is the lead khmer developer and community liaison. > >> > >> best, > >> ?titus > >> ----------------------------- > >> > >> Dr. C. Titus Brown, ctbrown@ucdavis.edu > >> Visiting Associate Prof., UC Davis > >> http://ged.msu.edu/ > >> _______________________________________________ > >> 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 -- C. Titus Brown, ctb@msu.edu From Enrico.Siragusa@fu-berlin.de Sun Nov 23 14:21:55 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XsX6u-001NI3-PZ>; Sun, 23 Nov 2014 14:21:52 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XsX6u-003xOA-NW>; Sun, 23 Nov 2014 14:21:52 +0100 Received: from cas2.campus.fu-berlin.de ([130.133.170.202]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XsX6u-003FY3-A0>; Sun, 23 Nov 2014 14:21:52 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS2.campus.fu-berlin.de ([130.133.170.202]) with mapi id 14.03.0210.002; Sun, 23 Nov 2014 14:21:51 +0100 From: "Siragusa, Enrico" To: SeqAn Development Thread-Topic: [Seqan-dev] Trouble Hashing Kmers into Qgram Index Thread-Index: AQHQA8L73oM0vrP8bka8VPHl4f0ZApxnz3oAgAJmmICAA/KEgA== Message-ID: References:

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Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Xt5Nv-003VXJ-0q>; Tue, 25 Nov 2014 02:57:43 +0100 Received: from mail-yk0-f175.google.com ([209.85.160.175]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1Xt5Nu-000Tzp-Rt>; Tue, 25 Nov 2014 02:57:42 +0100 Received: by mail-yk0-f175.google.com with SMTP id 200so4741837ykr.6 for ; Mon, 24 Nov 2014 17:57:40 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=5dpCy3xUH2GF8BXdcJHB0IOU5tUP83qtc7/iGHyjzSY=; b=XCeXC81ezcYUKf/Ov0RoOjluZECPp9IceVwQOIXGm5MLM1w8a1eKGwgMpTNt4BLE8e 10igfVRHHWJX4INTVqjbtK0jijeo+rH/8CTJmS/hxvQXfoGO4lLGFCfQyljL2yMKpYEX zTPTaCJHfWH5BNSunmgVSkPC0P0hvVz2A0ha0TdGZCJzXXh/aV4yr1jDi5ccmrYL6Yqt Zhb53FBoxchM+9SwWRQFRlc83itsPmzM/zYhS3KRT1V+ISR6eb/VlrOZ25JfJwgbyWnY tUfIPxWXZMf3Or8T0GN2i2G+0seq3kZI4hcHrjwNppOKSIPqIckbbVx7sSODi2O6UIb5 E4hQ== MIME-Version: 1.0 X-Received: by 10.236.24.161 with SMTP id x21mr21096255yhx.96.1416880660241; Mon, 24 Nov 2014 17:57:40 -0800 (PST) Received: by 10.170.110.19 with HTTP; Mon, 24 Nov 2014 17:57:40 -0800 (PST) Date: Mon, 24 Nov 2014 17:57:40 -0800 Message-ID: From: Brett Bowman To: SeqAn Development Content-Type: multipart/alternative; boundary=089e011831907165bf0508a53cfc X-Originating-IP: 209.85.160.175 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1416880663-00096E23-4B8CB7D6/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.477874, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=0.3 required=5.0 tests=FREEMAIL_FROM, HTML_IMAGE_ONLY_28,HTML_MESSAGE,RCVD_IN_DNSWL_LOW,RCVD_IN_MSPIKE_H2, T_DKIM_INVALID,T_REMOTE_IMAGE,URIBL_RHS_DOB X-Spam-Checker-Version: SpamAssassin 3.4.0 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Trouble Using Custom SeedSpec X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 25 Nov 2014 01:57:44 -0000 --089e011831907165bf0508a53cfc Content-Type: text/plain; charset=UTF-8 The algorithm I'm trying to implement with SeqAn (1.4.1) uses log-probabilities as scores, so I need to customize the Seed<> to change the default ScoreValue type: (Following the docs here: http://docs.seqan.de/seqan/1.4.2-dox/?p=SimpleSeed ) """ // Declare our Seed Config and associated Seed type struct SeedConfig { typedef size_t TPosition; typedef MakeSigned_::Type TDiagonal; typedef size_t TSize; typedef float TScoreValue; // Changed to Float to be compatible with existing scoring scheme }; typedef Seed TSeed; typedef SeedSet TSeedSet; """ But when I try to add seeds to my SeedSet, """ TSeed seed = TSeed(queryPos, refPos, 12); float score = 15.5; setScore(seed, score); std::cout << seed << " " << seqan::score(seed) << " " << score << std::endl; if (!addSeed(seeds, seed, 0, Merge())) { addSeed(seeds, seed, Single()); } """ I get the following error no matter what I try: """ /home/bbowman/git/SRSLI/src/C++/SparseAlignment.hpp:220:18: error: no matching function for call to 'addSeed' if (!addSeed(seeds, seed, 0, Merge())) ^~~~~~~ /usr/include/seqan/seeds/seeds_seed_set_unordered.h:361:1: note: candidate function [with TSeedSpec = SeedConfig, TDistanceThreshold = int] not viable: no known conversion from 'Seed' to 'const Seed' for 2nd argument addSeed(SeedSet & seedSet, """ What am I missing? Sincerely, Brett --089e011831907165bf0508a53cfc Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

The algorithm I'm trying to implement with SeqAn (1.4.= 1) uses log-probabilities as scores, so I need to customize the Seed<>= ; to change the default ScoreValue type:

(Following the docs here:=C2= =A0http://= docs.seqan.de/seqan/1.4.2-dox/?p=3DSimpleSeed)

"""

// Declare our Seed Config and associate= d Seed type

struct SeedConfig

{

=C2=A0 =C2=A0= typedef size_t TPosition;

=C2=A0 =C2=A0 typedef MakeSigned_<s= ize_t>::Type TDiagonal;

=C2=A0 =C2=A0 typedef size_t TSize= ;

=C2=A0 =C2=A0 typedef float TScoreValue; =C2=A0 // Changed to F= loat to be compatible with existing scoring scheme

};

<= br>

typedef Seed<Simple, SeedConfig> TSeed;

typed= ef SeedSet<SeedConfig> TSeedSet;

"""

But when I try to add seeds to my SeedSet,=C2=A0

"""

TSeed seed =3D TSeed(queryPos, re= fPos, 12);

float score =3D 15.5;

setScore(seed, score);=

std::cout << seed << " " << seqa= n::score(seed) << " " << score << std::endl;

=C2=A0

if (!addSeed(seeds, seed, 0, Merge()))

=C2=A0 =C2=A0 =C2=A0addSeed(seeds, seed, Single());

}<= /div>

"""

I get the = following error no matter what I try:

"""

/home/bbowman/git/SRSLI/src/C++/SparseAlignment.hpp:220:18: er= ror: no matching function for call to 'addSeed'

=C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 if (!addSeed(seeds, seed, 0, Merge()))

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0^~~~= ~~~

/usr/include/seqan/seeds/seeds_seed_set_unordered.h:361:1: no= te: candidate function [with TSeedSpec =3D SeedConfig, TDistanceThreshold = =3D int] not viable: no known conversion from

=C2=A0 =C2=A0 =C2= =A0 'Seed<Simple, struct SeedConfig>' to 'const Seed<s= truct SeedConfig, (default) struct seqan::DefaultSeedConfig>' for 2n= d argument

addSeed(SeedSet<TSeedSpec, Unordered> & seed= Set,

"""

What am I = missing?

Sincerely,

Brett

--089e011831907165bf0508a53cfc-- From NHTran@ntu.edu.sg Thu Nov 27 05:26:35 2014 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Xtqf3-002CxQ-Hm>; Thu, 27 Nov 2014 05:26:33 +0100 Received: from smtp4.ntu.edu.sg ([155.69.5.132]) by relay1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Xtqf2-0011x9-Rg>; Thu, 27 Nov 2014 05:26:33 +0100 X-AuditID: 9b450584-b7afeae000006267-22-5476a7f45ada Received: from EXSMTP6.staff.main.ntu.edu.sg ( [155.69.5.101]) by SMTP4.ntu.edu.sg (Symantec Messaging Gateway) with SMTP id BC.80.25191.4F7A6745; Thu, 27 Nov 2014 12:26:29 +0800 (MYT) Received: from EXCHHUB14.staff.main.ntu.edu.sg (155.69.25.17) by EXSMTP6.staff.main.ntu.edu.sg (155.69.5.101) with Microsoft SMTP Server (TLS) id 14.3.123.3; Thu, 27 Nov 2014 12:26:13 +0800 Received: from EXCHMBOX33.staff.main.ntu.edu.sg ([169.254.3.216]) by EXCHHUB14.staff.main.ntu.edu.sg ([155.69.25.17]) with mapi id 14.03.0123.003; Thu, 27 Nov 2014 12:26:28 +0800 From: "Tran Ngoc Hieu (Dr)" To: "seqan-dev@lists.fu-berlin.de" Thread-Topic: Failed to build FM index with hg19 Thread-Index: AdAJ+k9J9MYYafXVTs+FrI759VxrLA== Date: Thu, 27 Nov 2014 04:26:27 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_DA28F38A7BD3CF4799A3B54A9986CAFF013FAB631AEXCHMBOX33sta_" MIME-Version: 1.0 X-Brightmail-Tracker: H4sIAAAAAAAAA02Sf0gTUQDHefdjO5cX55zuNaPywCitaWlUEP2wBCEisRFZgZ7s2kZzjrtt OP/JrCQtJArFlvgbJQvFgalpWguKLGgqQplkqSkqCQoSI9PufKj77/O+v3jHPQpXt5M6ymJz 8IKNs7IKFfEkheT3LzW5DAktU+SRjvlnypMg1dv5SpEGLquOGXmrxcUL8cezVOavH7fYi3bl /egoVxaAwagSEEJBJgkG+oYViCOh/3urxCpKzbwEsDLgw9DhDYALbdU4OrwAsHVxnJQrCiYe rgTGgMwa5hQsvV+0NhXOxME5/y0c6QmwY+E5hlgPPcszhMwEEwPHvlYoZaaZDNjjRXkgXeNP P8rjjBaOTFZj6HoMbOj5jCOOgDMTKyTiaDg6+o1A+Vw40NaOo80w+OHx5JquZnbA0elC7AHQ eIJmPUEVT1AF6ftgTfeiAnEcbKydw9f50+sJLFivAcpmwFw4Z0hL0tscTj1vdOpFkxegv3O7 Ewwt632AoQAbSmtqXQY1yblEd44PbKMwNoKOrZekrdm5RreZE82ZgtPKiz4AKZzV0Lo6yaON nDufF3LXrSiKYLV0MXAa1IyJc/DXed7OC+vudopiIZ3VKBXDBN7E512zWB2bNkaFyOOh0vhD OUOLdi5HtJiQ3w+idVr6vGwwsmF22ja68mu7sbq6Ogu00qeE0xflVKj0Fjfas9IwJg1Hljnl YQe3aekKgGW+kq7ISdz9jpwHKWz6z5gh/NcVe/GdE6kjRLo/Kzm/y5tRurPPsMQfPXgv78ve 3yX+8szA4cGemuS73n/9U2fHmrrP9B4qea+ommrF4OTSQCLeW0FXX80+3VBLvC2vf9SSWFTY 9ne8+VJddsTNrsp89mmnuyrVUDa9Z5hzUywhmrkDsbggcv8BNHVP6kgDAAA= X-Originating-IP: 155.69.5.132 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1417062393-00096E23-53269413/0/0 X-Bogosity: Unsure, tests=bogofilter, spamicity=0.500658, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-0.8 required=5.0 tests=FU_BOGO_UNSURE, HTML_MESSAGE, RCVD_IN_DNSWL_MED X-Spam-Checker-Version: SpamAssassin 3.4.0 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Failed to build FM index with hg19 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 27 Nov 2014 04:26:35 -0000 --_000_DA28F38A7BD3CF4799A3B54A9986CAFF013FAB631AEXCHMBOX33sta_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear SeqAn Team, I often encounter the following error when trying to build the FM index of = the human genome (UCSC hg19) by using the tool "masai_indexer" or by follow= ing your online tutorial "MiniBowtie". The process sometimes runs smoothly,= but sometimes fails, thus I don't know what's going on. Everything is fine= with smaller genomes. Could you please give some advices? Thank you very m= uch! Building FM index... Asynchronous I/O operation failed (waitFor): "Success" fildes: 9 buffer: 7f7e3a5d6000 offset: 3298d0000 nbytes: 28000 event: 1 Raddr: 0x1def098 ../../core/include/seqan/file/file_page.h:740 FAILED! (WRITING operation c= ould not be completed: "Success") Aborted (core dumped) Regards, Hieu ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and = may be confidential and/or privileged. If you are not the intended recipien= t, please delete it, notify us and do not copy, use, or disclose its conten= ts. Towards a sustainable earth: Print only when necessary. Thank you. --_000_DA28F38A7BD3CF4799A3B54A9986CAFF013FAB631AEXCHMBOX33sta_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear SeqAn Team,

I often encounter the following error when trying to= build the FM index of the human genome (UCSC hg19) by using the tool ̶= 0;masai_indexer” or by following your online tutorial “MiniBowt= ie”. The process sometimes runs smoothly, but sometimes fails, thus I don’t know what’s going on. Everything is fine w= ith smaller genomes. Could you please give some advices? Thank you very muc= h!

Building FM index...

Asynchronous I/O operation failed (waitFor): "S= uccess"

fildes: 9

buffer: 7f7e3a5d6000

offset: 3298d0000

nbytes: 28000

event: 1

Raddr: 0x1def098

../../core/include/seqan/file/file_page.h:740 FAILED= ! (WRITING operation could not be completed: "Success")

Aborted (core dumped)

Regards,

Hieu

CONFIDENTIALITY: This email = is intended solely for the person(s) named and may be confidential and/or p= rivileged. If you are not the intended recipient, please delete it, notify = us and do not copy, use, or disclose its contents.
Towards a sustainable earth: Print only when necessary. Thank you. --_000_DA28F38A7BD3CF4799A3B54A9986CAFF013FAB631AEXCHMBOX33sta_-- From Enrico.Siragusa@fu-berlin.de Thu Nov 27 14:48:52 2014 Received: from outpost9.zedat.fu-berlin.de ([130.133.4.95]) by list1.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XtzRC-002uGW-2C>; Thu, 27 Nov 2014 14:48:50 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1XtzRC-003AhS-0y>; Thu, 27 Nov 2014 14:48:50 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.82) for seqan-dev@lists.fu-berlin.de with esmtps (envelope-from ) id <1XtzRB-000lLg-NM>; Thu, 27 Nov 2014 14:48:50 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS3.campus.fu-berlin.de ([130.133.170.203]) with mapi id 14.03.0210.002; Thu, 27 Nov 2014 14:48:48 +0100 From: "Siragusa, Enrico" To: SeqAn Development Thread-Topic: [Seqan-dev] Failed to build FM index with hg19 Thread-Index: AdAJ+k9J9MYYafXVTs+FrI759VxrLAARjLGA Message-ID: <9813C5E1-B4CE-4F7B-A01E-CD7DF2B5A912@fu-berlin.de> References: In-Reply-To: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_9813C5E1B4CE4F7BA01ECD7DF2B5A912fuberlinde_" MIME-Version: 1.0 Date: Thu, 27 Nov 2014 14:48:48 +0100 X-Original-Date: Thu, 27 Nov 2014 13:48:48 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: XA X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1417096130-00096E23-2CF044EC/0/0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.4 X-Spam-Flag: NO X-Spam-Status: No, score=-50.0 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.4.0 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Failed to build FM index with hg19 X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.16 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, 27 Nov 2014 13:48:52 -0000 --_000_9813C5E1B4CE4F7BA01ECD7DF2B5A912fuberlinde_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi Hieu, This incomprehensible error message means that the index construction algor= ithm run out of disk space! The suffix array construction algorithm impleme= nted in SeqAn (Skew7) works on external memory and requires at least 20-25 = times the disk space of the input text. The algorithm writes such temporary= data to the system=92s temporary folder (usually /tmp). In general, you ca= n change this folder by (re)defining the environment variable TMPDIR. Concerning any application that you write using SeqAn (or the MiniBowtie de= mo): you should redefine the SAValue metafunction to squeeze the size of th= e suffix array. By default, SAValue is a Pair<__uint64, __uint64>. For hg19= , you can redefine SAValue as follows: namespace seqan { template struct SAValue > { typedef Pair<__uint8, __uint32, Pack> Type; }; } In this way each SA value will consume only 5 bytes (1 byte to index any se= quence in the text collection + 4 bytes to index any position within any se= quence). Concerning Masai: please upgrade to Yara (http://www.seqan.de/projects/yara= /) if you didn=92t! Enrico On 27 Nov 2014, at 05:26, Tran Ngoc Hieu (Dr) > wrote: Dear SeqAn Team, I often encounter the following error when trying to build the FM index of = the human genome (UCSC hg19) by using the tool =93masai_indexer=94 or by fo= llowing your online tutorial =93MiniBowtie=94. The process sometimes runs s= moothly, but sometimes fails, thus I don=92t know what=92s going on. Everyt= hing is fine with smaller genomes. Could you please give some advices? Than= k you very much! Building FM index... Asynchronous I/O operation failed (waitFor): "Success" fildes: 9 buffer: 7f7e3a5d6000 offset: 3298d0000 nbytes: 28000 event: 1 Raddr: 0x1def098 ../../core/include/seqan/file/file_page.h:740 FAILED! (WRITING operation c= ould not be completed: "Success") Aborted (core dumped) Regards, Hieu ________________________________ CONFIDENTIALITY: This email is intended solely for the person(s) named and = may be confidential and/or privileged. If you are not the intended recipien= t, please delete it, notify us and do not copy, use, or disclose its conten= ts. Towards a sustainable earth: Print only when necessary. Thank you. ________= _______________________________________ seqan-dev mailing list seqan-dev@lists.fu-berlin.de https://lists.fu-berlin.de/listinfo/seqan-dev --_000_9813C5E1B4CE4F7BA01ECD7DF2B5A912fuberlinde_ Content-Type: text/html; charset="Windows-1252" Content-ID: <369F6B03DCAD244CB30252D97E02F373@campus.fu-berlin.de> Content-Transfer-Encoding: quoted-printable Hi Hieu,

This incomprehensible error message means that the index construction = algorithm run out of disk space! The suffix array construction algorithm im= plemented in SeqAn (Skew7) works on external memory and requires at least 2= 0-25 times the disk space of the input text. The algorithm writes such temporary data to the system=92s tem= porary folder (usually /tmp). In general, you can change this folder by (re= )defining the environment variable TMPDIR.

Concerning any application that you write using SeqAn (or the MiniBowt= ie demo): you should redefine the SAValue metafunction to squeeze the size = of the suffix array. By default, SAValue is a Pair<__uint64, __uint64>= ;. For hg19, you can redefine SAValue as follows:

namespace seqan {

template <typename TString, typename TSpec>

struct SAValue<StringSet<TString, TSpec&g= t; >

{

&nb= sp; typedef Pair<__uint8, __uint32, Pack> Type;

};

}

In this way each SA value will consume only 5 bytes (1 byte to index a= ny sequence in the text collection + 4 bytes to index any position with= in any sequence).

Concerning Masai: please upgrade to Yara (http://www.seqan.de/projects/yara/) if you didn=92t!=

Enrico

On 27 Nov 2014, at 05:26, Tran Ngoc Hieu (Dr) <NHTran@ntu.edu.sg> wrote:

Dear SeqAn Team,

I often encounter the following error when trying to build the FM index of = the human genome (UCSC hg19) by using the tool =93masai_indexer=94 or by fo= llowing your online tutorial =93MiniBowtie=94. The process sometimes runs s= moothly, but sometimes fails, thus I don=92t know what=92s going on. Everything is fine with smaller genomes. Could you= please give some advices? Thank you very much!

Building FM index...

Asynchronous I/O operation failed (waitFor): "Success"

fildes: 9

buffer: 7f7e3a5d6000

offset: 3298d0000

nbytes: 28000

event: 1

Raddr: 0x1def098

../../core/include/seqan/file/file_page.h:740 FAILED! (WRITING operat= ion could not be completed: "Success")

Aborted (core dumped)

Regards,

Hieu

CONFIDENTIALITY: This email = is intended solely for the person(s) named and may be confidential and/or p= rivileged. If you are not the intended recipient, please delete it, notify = us and do not copy, use, or disclose its contents.
Towards a sustainable earth: Print only when necessary. Thank you. __________________________= _____________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seq= an-dev

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