From jose.ig.miranda@gmail.com Thu Nov 01 02:36:56 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TTjiF-003IJP-HL>; Thu, 01 Nov 2012 02:36:51 +0100 Received: from mail-la0-f54.google.com ([209.85.215.54]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TTjiF-00115M-Ek>; Thu, 01 Nov 2012 02:36:51 +0100 Received: by mail-la0-f54.google.com with SMTP id e12so1894443lag.13 for ; Wed, 31 Oct 2012 18:36:50 -0700 (PDT) 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=mSz2kADryVmqQkfnb0wNp5BfV9PJcqbtR4yAoWqEOsw=; b=xCuhefTtjURuAMlh9DTLbnaa/EeyWema1CDMQtmMLiNtqwoKoFPBiZNFsbcSgi6cwn o6Kf0c4/FhzXPSAUSzHT7quxsa6AGFr9X3+QqBdsZkC4vUIpV1Ir+XBDFTtmnVPTGHPG sH8pX+TgsHrz6AGKdWGAHj02wTu6mJBX7UGJhnmsdRs/idokiC7hKJDxtILOQomC/Hfu Y/O4xrjoXwV78q2LTwRmVGD0Hc1jYWzvcJqqJpnNcWgCV8SJaXl6MdqQt7V+1ffDyWCq RJmbz5TwNhX08OifVuYmNzgwouklORqWp5VuEfGQagR8NCCch+fIOFsX8EbnQoa20Pik 8e+w== MIME-Version: 1.0 Received: by 10.112.48.71 with SMTP id j7mr13083438lbn.57.1351733809949; Wed, 31 Oct 2012 18:36:49 -0700 (PDT) Received: by 10.114.5.225 with HTTP; Wed, 31 Oct 2012 18:36:49 -0700 (PDT) Date: Wed, 31 Oct 2012 23:36:49 -0200 Message-ID: From: =?ISO-8859-1?Q?Jos=E9_Iguelmar_Miranda?= To: seqan-dev@lists.fu-berlin.de Content-Type: multipart/alternative; boundary=bcaec55556ac92ac9204cd650d75 X-Originating-IP: 209.85.215.54 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1351733811-0000097C-C0A212F9/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000006, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.2 on Dschibuti.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] Some SeqAn problems X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 01 Nov 2012 01:36:56 -0000 --bcaec55556ac92ac9204cd650d75 Content-Type: text/plain; charset=ISO-8859-1 Hi: First and foremost, my best congratulations for this wonderful C++ library. SeqAn is an awesome contribution to sequence analysis. You guys are great! I installed SeqAn in my MBP-intel using MacPorts. Almost everything runs smooth. But I am stuck with some problems: 1. In the tutorial PairwiseSequenceAlignment I got problems with the use of LocalAlignmentEnumerator, Banded alignment (two last parms values) and globalAlignmentScore. The compiler error msg is "xxx was not declared in this scope." Indeed, I double checked the headers and the ones corresponding to these statements aren't available in the includes (/opt/local/include/seqan/). 2. The same happens with FMIndex (was not declared in this scope). 3. In the graph tutorial, the same happens with assignVertexMap (was not declared in this scope). Searching your sources, I could find the headers for these statements. Would it be a problem with the MacPorts installation? Best regards. Jose I Miranda. --bcaec55556ac92ac9204cd650d75 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi:

First and foremost, my best congratulations for this= wonderful C++ library. SeqAn is an awesome contribution to sequence analys= is. You guys are great!

I installed SeqAn in my MB= P-intel using MacPorts. Almost everything runs smooth. But I am stuck with = some problems:

1. In the tutorial PairwiseSequenceAlignment I got prob= lems with the use of LocalAlignmentEnumerator, Banded alignment (two last p= arms values) and globalAlignmentScore. The compiler error msg is "xxx = was not declared in this scope." Indeed, I double checked the headers = and the ones corresponding to these statements aren't available in the = includes (/opt/local/include/seqan/).

2. The same happens with FMIndex=A0(was not declared in= this scope).

3. In the graph tutorial, the same h= appens with assignVertexMap (was not declared in this scope).
Searching your sources, I could find the headers for these state= ments. Would it be a problem with the MacPorts installation?

=
Best regards.
Jose I Miranda.

--bcaec55556ac92ac9204cd650d75-- From fredrik.boulund@chalmers.se Thu Nov 01 13:44:45 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TTu8Z-001QrR-99>; Thu, 01 Nov 2012 13:44:43 +0100 Received: from liara.ita.chalmers.se ([129.16.226.167]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TTu8Y-002HOo-WC>; Thu, 01 Nov 2012 13:44:43 +0100 Received: from [129.16.127.42] (129.16.127.42) by smtp.chalmers.se (129.16.10.240) with Microsoft SMTP Server (TLS) id 14.2.318.4; Thu, 1 Nov 2012 13:44:40 +0100 Message-ID: <50926EBA.2050106@chalmers.se> Date: Thu, 1 Nov 2012 13:44:42 +0100 From: Fredrik Boulund User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:16.0) Gecko/20121026 Thunderbird/16.0.2 MIME-Version: 1.0 To: Content-Type: multipart/mixed; boundary="------------040500060603050600000500" X-Originating-IP: 129.16.226.167 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1351773883-0000097C-A2269A6B/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.393698, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=0.0 required=5.0 tests=HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.2 on Burundi.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] RazerS3 result duplication and other issues X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 Precedence: list Reply-To: fredrik.boulund@chalmers.se, SeqAn Development List-Id: SeqAn Development List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 01 Nov 2012 12:44:46 -0000 --------------040500060603050600000500 Content-Type: multipart/alternative; boundary="------------060905060802060304000803" --------------060905060802060304000803 Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Content-Transfer-Encoding: 7bit Hi, I'm trying to use RazerS3 in a project were I want to map reads to contigs and I'm putting RazerS3 in an automated pipeline written in Python. The version of RazerS3 I'm currently using is: VERSION razers3 version: 3.1 [12568] Last update 2012-08-20 This was the most recent binary on the SeqAn website. I have also compiled RazerS3 from sources (razers3 version: 3.1 [12787] Last update 2012-09-03) but the same problems exist there. First off, a minor annoyance, RazerS3 produces some output to stderr when running the program that seems a bit like some kind of debugging information rather than information for the user. This looks something like this, and is shown every time the program is run: useExternalSort == 0 useSequentialCompaction == 0 length(threadLocalStorages[0].matches) == 20 length(store.alignedReadStore) == 20 Second, a bit more severe; it seems that RazerS3 is producing duplicate output in some cases for the same read mapped to the same contig (in the same position). Is this intended or just a "feature"? Attached you'll find a zip-file with contigs and reads that reproduce the errors. In some cases this also is worsened when running RazerS3 multithreaded (i.e. using the -tc commandline option). When running multithreaded we sometimes see an increase in the amount of duplicates in the output, but it also seems to be a lot slower (sometimes even taking even substantially more time than running it single-threaded) but still consuming cpu-time for each thread as if it's actually doing the entire alignment N number of times (N = number of cores chosen). Very strange. I'm sorry to say that I unfortunately haven't been able to replicate this behavior in such small files that can be easily attached to email. Below is an example using the attached files to illustrate what I mean about the duplications (and the non-user-friendly debug-looking output that is printed to stderr on program exit). [example]$ ls contigs.fa reads.fs [example]$ razers3 razers3 - Fast Read Mapping with Sensitivity Control ==================================================== razers3 [OPTIONS] razers3 [OPTIONS] Try 'razers3 --help' for more information. VERSION razers3 version: 3.1 [12568] Last update 2012-08-20 [example]$ razers3 contigs.fa reads.fa useExternalSort == 0 useSequentialCompaction == 0 length(threadLocalStorages[0].matches) == 20 length(store.alignedReadStore) == 20 [example]$ cat reads.fa.results read1 0 75 F contig1 0 75 100 read1 0 75 F contig1 0 75 100 read1 0 75 F contig3 0 74 98.667 read1 0 75 F contig3 0 74 98.667 read1 0 75 F contig3 0 74 98.667 read1 0 75 R contig4 582 657 100 read2 0 67 F contig1 0 67 100 read2 0 67 F contig1 0 67 100 read2 0 67 F contig3 0 66 98.507 read2 0 67 F contig3 0 66 98.507 read2 0 67 F contig3 0 66 98.507 read2 0 67 R contig4 590 657 100 read3 0 72 F contig1 0 75 95.833 read3 0 72 F contig1 0 75 95.833 read3 0 72 R contig4 582 657 95.833 read4 0 65 F contig1 5 70 100 read4 0 65 F contig2 0 64 98.462 read4 0 65 F contig3 4 69 100 read4 0 65 F contig3 4 69 100 read4 0 65 R contig4 587 652 100 As you can see there are several duplicates of identical mappings (for example the first to rows). This seems to be alleviated by using "-m 1", outputting only the best match for each read, although this is not desirable in my case. I hope any of the information helps you figure out the issues. I also have a couple of questions on how RazerS3 reads the files. Would it be possible for RazerS3 to accept reads from a stream or FIFO? I made some tests and had a quick glance in the source code and it appears that RazerS3 tries to seek in the reads-file at some point, breaking my pipe. I sincerely hope that it does not read the entire reads-file into memory at any point, since I'm concerned that it'll start swapping if I load large data sets. Do you have any tips here to help me out? Best regards Fredrik Boulund -- ------------------------------------------------------------------------------------------------------------------------------------------------------ Fredrik Boulund, PhD student Department of Mathematical Sciences Division of Mathematical Statistics Chalmers University of Technology, SE-412 96 Gothenburg, Sweden Email: fredrik.boulund@chalmers.se Phone: +46(0)31-772-5342, mobile +46(0)73-770 6629 ------------------------------------------------------------------------------------------------------------------------------------------------------ --------------060905060802060304000803 Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: 7bit Hi,

I'm trying to use RazerS3 in a project were I want to map reads to contigs and I'm putting RazerS3 in an automated pipeline written in Python.
The version of RazerS3 I'm currently using is:
VERSION                                                             
    razers3 version: 3.1 [12568]                                    
    Last update 2012-08-20                                          
This was the most recent binary on the SeqAn website. I have also compiled RazerS3 from sources (razers3 version: 3.1 [12787] Last update 2012-09-03) but the same problems exist there.

First off, a minor annoyance, RazerS3 produces some output to stderr when running the program that seems a bit like some kind of debugging information rather than information for the user.
This looks something like this, and is shown every time the program is run:
useExternalSort == 0                      
useSequentialCompaction == 0              
length(threadLocalStorages[0].matches) == 20
length(store.alignedReadStore) == 20  

Second, a bit more severe; it seems that RazerS3 is producing duplicate output in some cases for the same read mapped to the same contig (in the same position). Is this intended or just a "feature"? Attached you'll find a zip-file with contigs and reads that reproduce the errors.
In some cases this also is worsened when running RazerS3 multithreaded (i.e. using the -tc commandline option). When running multithreaded we sometimes see an increase in the amount of duplicates in the output, but it also seems to be a lot slower (sometimes even taking even substantially more time than running it single-threaded) but still consuming cpu-time for each thread as if it's actually doing the entire alignment N number of times (N = number of cores chosen). Very strange. I'm sorry to say that I unfortunately haven't been able to replicate this behavior in such small files that can be easily attached to email.

Below is an example using the attached files to illustrate what I mean about the duplications (and the non-user-friendly debug-looking output that is printed to stderr on program exit).

[example]$ ls
contigs.fa reads.fs

[example]$ razers3
razers3 - Fast Read Mapping with Sensitivity Control                
====================================================                
    razers3 [OPTIONS] <GENOME FILE> <READS FILE>                    
    razers3 [OPTIONS] <GENOME FILE> <PE-READS FILE1> <PE-READS FILE2>
    Try 'razers3 --help' for more information.                      
                                                                    
VERSION                                                             
    razers3 version: 3.1 [12568]                                    
    Last update 2012-08-20                                          

[example]$ razers3 contigs.fa reads.fa
useExternalSort == 0                      
useSequentialCompaction == 0              
length(threadLocalStorages[0].matches) == 20
length(store.alignedReadStore) == 20                

[example]$ cat reads.fa.results
read1   0       75      F       contig1 0       75      100  
read1   0       75      F       contig1 0       75      100  
read1   0       75      F       contig3 0       74      98.667
read1   0       75      F       contig3 0       74      98.667
read1   0       75      F       contig3 0       74      98.667
read1   0       75      R       contig4 582     657     100  
read2   0       67      F       contig1 0       67      100  
read2   0       67      F       contig1 0       67      100  
read2   0       67      F       contig3 0       66      98.507
read2   0       67      F       contig3 0       66      98.507
read2   0       67      F       contig3 0       66      98.507
read2   0       67      R       contig4 590     657     100  
read3   0       72      F       contig1 0       75      95.833
read3   0       72      F       contig1 0       75      95.833
read3   0       72      R       contig4 582     657     95.833
read4   0       65      F       contig1 5       70      100  
read4   0       65      F       contig2 0       64      98.462
read4   0       65      F       contig3 4       69      100  
read4   0       65      F       contig3 4       69      100  
read4   0       65      R       contig4 587     652     100  

As you can see there are several duplicates of identical mappings (for example the first to rows). This seems to be alleviated by using "-m 1", outputting only the best match for each read, although this is not desirable in my case.

I hope any of the information helps you figure out the issues.

I also have a couple of questions on how RazerS3 reads the files. Would it be possible for RazerS3 to accept reads from a stream or FIFO? I made some tests and had a quick glance in the source code and it appears that RazerS3 tries to seek in the reads-file at some point, breaking my pipe. I sincerely hope that it does not read the entire reads-file into memory at any point, since I'm concerned that it'll start swapping if I load large data sets. Do you have any tips here to help me out?

Best regards

Fredrik Boulund 
-- 
——————————————————————————————————————————————————
Fredrik Boulund, PhD student
Department of Mathematical Sciences
Division of Mathematical Statistics
Chalmers University of Technology, 
SE-412 96 Gothenburg, Sweden
Email: fredrik.boulund@chalmers.se 
Phone: +46(0)31-772-5342, mobile +46(0)73-770 6629
——————————————————————————————————————————————————
--------------060905060802060304000803-- --------------040500060603050600000500 Content-Type: application/x-zip-compressed; name="example.zip" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="example.zip" UEsDBBQAAAAAABWRREEAAAAAAAAAAAAAAAAIAAAAZXhhbXBsZS9QSwMEFAAAAAgAgI5EQfwH WyneAQAAOAgAABIAAABleGFtcGxlL2NvbnRpZ3MuZmHtlDtSBDEMRPO5DZ+YKpcCX8A3IKBI IOH+RfdraSElgIjZHa/1a7VkeZ+e398+Xl/urnX2Xmcdf71Zax8/tXZpv2S1JLl2VYtS6y2t hbdM+p6sx1i24WOkq7PdX7+bR3pFeZVZoAKJ5NBOsVv01iRqb1DlQIQDBu0Qriin1Ocbmn0L Jvwc05FG+q6pkZaMsSmjy8S6KQzkQGnfsbILUwqtiMt6vWsKdLeU0SQBdwVuRcAsuKNiBcNw 7mZWU4Szy28ajsFDTzhLF8dA1TTK9DhAU9R+j7VwsGQaiKndWh+hGIeVqyOhY7Ocrz4PNKKy y+5TgUbOqMW4dylMUUhPVm2gaq2PW2uPjiIlzVA+XH9wA/4n838yfzyZj5ea5FyNQssWNWQg tLNeGypulEW1YWF/PT1kLSopyVFK1ibuNMR+lUU/jqYAzpvD2JNVBmogZPrsw7TpBm2r3rkg kjJzIQ373CBOmP4y5lTXjsTicZvXFJpbw2Fxh52IqmDlCT1MIMQUzCK9n5ll0xtkKw5gTaPA 1uY2r9Nx/aSixLbNJdCH3EKsGQPalT6nhMRujHNGc+crDZlwbzNkX2iSg5HrELScGrWu+Q/J SpFMPj56g2mTC25RoCDh3f9jxvJGWa9PUEsDBBQAAAAIAHeOREHR9jNMUwAAADcBAAAQAAAA ZXhhbXBsZS9yZWFkcy5mYa2PTQqAUAiE996mn3UwzGIu4AWCukD3XzS+WkZQPFFxVD50OfZ1 GwIpIZHlVQDKMkJ0DU9LWVPkLd120Jlt2yN7NOTYA3mhpj+ol9Pm+IZ6eDROUEsDBBQAAAAI ABCRREHvVr38jQAAAIICAAAXAAAAZXhhbXBsZS9yZWFkcy5mYS5yZXN1bHStkU0OgkAMRtf1 MKR0+jNzAQ/gDYwa40YT4/0jHYkU2ABh2fnepK/t+3a+toBgAke4vJ6fx70vW8TD6jR5yVBy o2r7AqceYJBMoGJ/B+oAtZGhbkyTl+rdBW1fIPgXHPnXkWm64SJNTmkVMFtRZNg14h0FDH8O 87Q61yuwUgSGMRm0+PfladSz7oEq8AVQSwECPwAUAAAAAAAVkURBAAAAAAAAAAAAAAAACAAk AAAAAAAAABAAAAAAAAAAZXhhbXBsZS8KACAAAAAAAAEAGACHt/iESqLNAYe3+IRKos0BrdnC hEqizQFQSwECPwAUAAAACACAjkRB/AdbKd4BAAA4CAAAEgAkAAAAAAAAACAAAAAmAAAAZXhh bXBsZS9jb250aWdzLmZhCgAgAAAAAAABABgAAJCUMEiizQGAU14ySKLNAZio44RKos0BUEsB Aj8AFAAAAAgAd45EQdH2M0xTAAAANwEAABAAJAAAAAAAAAAgAAAANAIAAGV4YW1wbGUvcmVh ZHMuZmEKACAAAAAAAAEAGACAvqMnSKLNAYAYBipIos0B7DXPhEqizQFQSwECPwAUAAAACAAQ kURB71a9/I0AAACCAgAAFwAkAAAAAAAAACAAAAC1AgAAZXhhbXBsZS9yZWFkcy5mYS5yZXN1 bHQKACAAAAAAAAEAGAAAwNt/SqLNAQDA239Kos0Bh7f4hEqizQFQSwUGAAAAAAQABACJAQAA dwMAAAAA --------------040500060603050600000500-- From manuel.holtgrewe@fu-berlin.de Wed Nov 14 22:21:05 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TYkON-0049pj-O0>; Wed, 14 Nov 2012 22:21:03 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1TYkON-0043x2-HM>; Wed, 14 Nov 2012 22:21:03 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.69) with esmtp (envelope-from ) id <1TYkON-000DTq-3v>; Wed, 14 Nov 2012 22:21:03 +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 14.02.0318.004; Wed, 14 Nov 2012 22:21:01 +0100 From: "Holtgrewe, Manuel" To: "fredrik.boulund@chalmers.se" , "SeqAn Development" Thread-Topic: [Seqan-dev] RazerS3 result duplication and other issues Thread-Index: AQHNuC6zcFvveMJvWkiUH1KVwGpwB5fp6q21 Message-ID: References: <50926EBA.2050106@chalmers.se> In-Reply-To: <50926EBA.2050106@chalmers.se> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: multipart/alternative; boundary="_000_FCCAB9D80C3DAB47B5601C5B0E62872B19A66B9Dex02acampusfube_" MIME-Version: 1.0 Date: Wed, 14 Nov 2012 22:21:00 +0100 X-Original-Date: Wed, 14 Nov 2012 21:21:00 +0000 X-Originating-IP: 130.133.170.203 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1352928063-0000097C-2F627502/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.016480, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.2 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] RazerS3 result duplication and other issues X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 14 Nov 2012 21:21:05 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B19A66B9Dex02acampusfube_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Der Fredrik, sorry for not getting back to you earlier. I removed the errorneous message, thank you for reporting this. We will look into the duplication issue as soon as possible. However, becau= se of deadlines I have to ask you for a bit more patience regarding this is= sue. Cheers, Manuel ________________________________ From: Fredrik Boulund [fredrik.boulund@chalmers.se] Sent: Thursday, November 01, 2012 1:44 PM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] RazerS3 result duplication and other issues Hi, I'm trying to use RazerS3 in a project were I want to map reads to contigs = and I'm putting RazerS3 in an automated pipeline written in Python. The version of RazerS3 I'm currently using is: VERSION razers3 version: 3.1 [12568] Last update 2012-08-20 This was the most recent binary on the SeqAn website. I have also compiled = RazerS3 from sources (razers3 version: 3.1 [12787] Last update 2012-09-03) = but the same problems exist there. First off, a minor annoyance, RazerS3 produces some output to stderr when r= unning the program that seems a bit like some kind of debugging information= rather than information for the user. This looks something like this, and is shown every time the program is run: useExternalSort =3D=3D 0 useSequentialCompaction =3D=3D 0 length(threadLocalStorages[0].matches) =3D=3D 20 length(store.alignedReadStore) =3D=3D 20 Second, a bit more severe; it seems that RazerS3 is producing duplicate out= put in some cases for the same read mapped to the same contig (in the same = position). Is this intended or just a "feature"? Attached you'll find a zip= -file with contigs and reads that reproduce the errors. In some cases this also is worsened when running RazerS3 multithreaded (i.e= . using the -tc commandline option). When running multithreaded we sometime= s see an increase in the amount of duplicates in the output, but it also se= ems to be a lot slower (sometimes even taking even substantially more time = than running it single-threaded) but still consuming cpu-time for each thre= ad as if it's actually doing the entire alignment N number of times (N =3D = number of cores chosen). Very strange. I'm sorry to say that I unfortunatel= y haven't been able to replicate this behavior in such small files that can= be easily attached to email. Below is an example using the attached files to illustrate what I mean abou= t the duplications (and the non-user-friendly debug-looking output that is = printed to stderr on program exit). [example]$ ls contigs.fa reads.fs [example]$ razers3 razers3 - Fast Read Mapping with Sensitivity Control =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D razers3 [OPTIONS] razers3 [OPTIONS] Try 'razers3 --help' for more information. VERSION razers3 version: 3.1 [12568] Last update 2012-08-20 [example]$ razers3 contigs.fa reads.fa useExternalSort =3D=3D 0 useSequentialCompaction =3D=3D 0 length(threadLocalStorages[0].matches) =3D=3D 20 length(store.alignedReadStore) =3D=3D 20 [example]$ cat reads.fa.results read1 0 75 F contig1 0 75 100 read1 0 75 F contig1 0 75 100 read1 0 75 F contig3 0 74 98.667 read1 0 75 F contig3 0 74 98.667 read1 0 75 F contig3 0 74 98.667 read1 0 75 R contig4 582 657 100 read2 0 67 F contig1 0 67 100 read2 0 67 F contig1 0 67 100 read2 0 67 F contig3 0 66 98.507 read2 0 67 F contig3 0 66 98.507 read2 0 67 F contig3 0 66 98.507 read2 0 67 R contig4 590 657 100 read3 0 72 F contig1 0 75 95.833 read3 0 72 F contig1 0 75 95.833 read3 0 72 R contig4 582 657 95.833 read4 0 65 F contig1 5 70 100 read4 0 65 F contig2 0 64 98.462 read4 0 65 F contig3 4 69 100 read4 0 65 F contig3 4 69 100 read4 0 65 R contig4 587 652 100 As you can see there are several duplicates of identical mappings (for exam= ple the first to rows). This seems to be alleviated by using "-m 1", output= ting only the best match for each read, although this is not desirable in m= y case. I hope any of the information helps you figure out the issues. I also have a couple of questions on how RazerS3 reads the files. Would it = be possible for RazerS3 to accept reads from a stream or FIFO? I made some = tests and had a quick glance in the source code and it appears that RazerS3= tries to seek in the reads-file at some point, breaking my pipe. I sincere= ly hope that it does not read the entire reads-file into memory at any poin= t, since I'm concerned that it'll start swapping if I load large data sets.= Do you have any tips here to help me out? Best regards Fredrik Boulund -- =97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97= =97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97 Fredrik Boulund, PhD student Department of Mathematical Sciences Division of Mathematical Statistics Chalmers University of Technology, SE-412 96 Gothenburg, Sweden Email: fredrik.boulund@chalmers.se Phone: +46(0)31-772-5342, mobile +46(0)73-770 6629 =97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97= =97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B19A66B9Dex02acampusfube_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Der Fredrik,

sorry for not getting back to you earlier.

I removed the errorneous message, thank you for reporting this.

We will look into the duplication issue as soon as possible. However, = because of deadlines I have to ask you for a bit more patience regarding th= is issue.

Cheers,
Manuel

From: Fredrik Boulund [fredrik.boulund@ch= almers.se]
Sent: Thursday, November 01, 2012 1:44 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] RazerS3 result duplication and other issues

Hi,

I'm trying to use RazerS3 in a project were I want to map reads to contigs = and I'm putting RazerS3 in an automated pipeline written in Python.
The version of RazerS3 I'm currently using is:
VERSION          &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;
    razers3 version: 3.1 [12568]   &= nbsp;           &nbs= p;            &= nbsp;       
    Last update 2012-08-20    &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;
This was the most recent binary on the SeqAn website. I have also compiled = RazerS3 from sources (razers3 version: 3.1 [12787] Last update 2012-09-03) = but the same problems exist there.

First off, a minor annoyance, RazerS3 produces some output to stderr when r= unning the program that seems a bit like some kind of debugging information= rather than information for the user.
This looks something like this, and is shown every time the program is run:=
useExternalSort =3D=3D 0      &nbs= p;            &= nbsp;  
useSequentialCompaction =3D=3D 0     &nbs= p;        
length(threadLocalStorages[0].matches) =3D=3D 20
length(store.alignedReadStore) =3D=3D 20   =

Second, a bit more severe; it seems that RazerS3 is producing duplicate out= put in some cases for the same read mapped to the same contig (in the same = position). Is this intended or just a "feature"? Attached you'll = find a zip-file with contigs and reads that reproduce the errors.
In some cases this also is worsened when running RazerS3 multithreaded (i.e= . using the -tc commandline option). When running multithreaded we sometime= s see an increase in the amount of duplicates in the output, but it also se= ems to be a lot slower (sometimes even taking even substantially more time than running it single-threaded) = but still consuming cpu-time for each thread as if it's actually doing the = entire alignment N number of times (N =3D number of cores chosen). Very str= ange. I'm sorry to say that I unfortunately haven't been able to replicate this behavior in such small files that can = be easily attached to email.

Below is an example using the attached files to illustrate what I mean abou= t the duplications (and the non-user-friendly debug-looking output that is = printed to stderr on program exit).

[example]$ ls
contigs.fa reads.fs

[example]$ razers3
razers3 - Fast Read Mapping with Sensitivity Control  &n= bsp;            = ; 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D          =       
    razers3 [OPTIONS] <GENOME FILE> <READS= FILE>           =          
    razers3 [OPTIONS] <GENOME FILE> <PE-RE= ADS FILE1> <PE-READS FILE2>
    Try 'razers3 --help' for more information. = ;            &n= bsp;        
           =             &nb= sp;            =             &nb= sp;            =        
VERSION          = ;            &n= bsp;            = ;            &n= bsp;            = ; 
    razers3 version: 3.1 [12568]   &= nbsp;           &nbs= p;            &= nbsp;       
    Last update 2012-08-20    &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;

[example]$ razers3 contigs.fa reads.fa
useExternalSort =3D=3D 0       =             &nb= sp;  
useSequentialCompaction =3D=3D 0     &nbs= p;        
length(threadLocalStorages[0].matches) =3D=3D 20
length(store.alignedReadStore) =3D=3D 20       = ;         

[example]$ cat reads.fa.results
read1   0       75 &n= bsp;    F       contig1 0 = ;      75      100 &= nbsp;
read1   0       75 &n= bsp;    F       contig1 0 = ;      75      100 &= nbsp;
read1   0       75 &n= bsp;    F       contig3 0 = ;      74      98.667
read1   0       75 &n= bsp;    F       contig3 0 = ;      74      98.667
read1   0       75 &n= bsp;    F       contig3 0 = ;      74      98.667
read1   0       75 &n= bsp;    R       contig4 582&nb= sp;    657     100   =
read2   0       67 &n= bsp;    F       contig1 0 = ;      67      100 &= nbsp;
read2   0       67 &n= bsp;    F       contig1 0 = ;      67      100 &= nbsp;
read2   0       67 &n= bsp;    F       contig3 0 = ;      66      98.507
read2   0       67 &n= bsp;    F       contig3 0 = ;      66      98.507
read2   0       67 &n= bsp;    F       contig3 0 = ;      66      98.507
read2   0       67 &n= bsp;    R       contig4 590&nb= sp;    657     100   =
read3   0       72 &n= bsp;    F       contig1 0 = ;      75      95.833
read3   0       72 &n= bsp;    F       contig1 0 = ;      75      95.833
read3   0       72 &n= bsp;    R       contig4 582&nb= sp;    657     95.833
read4   0       65 &n= bsp;    F       contig1 5 = ;      70      100 &= nbsp;
read4   0       65 &n= bsp;    F       contig2 0 = ;      64      98.462
read4   0       65 &n= bsp;    F       contig3 4 = ;      69      100 &= nbsp;
read4   0       65 &n= bsp;    F       contig3 4 = ;      69      100 &= nbsp;
read4   0       65 &n= bsp;    R       contig4 587&nb= sp;    652     100  

As you can see there are several duplicates of identical mappings (for exam= ple the first to rows). This seems to be alleviated by using "-m 1&quo= t;, outputting only the best match for each read, although this is not desi= rable in my case.

I hope any of the information helps you figure out the issues.

I also have a couple of questions on how RazerS3 reads the files. Would it = be possible for RazerS3 to accept reads from a stream or FIFO? I made some = tests and had a quick glance in the source code and it appears that RazerS3= tries to seek in the reads-file at some point, breaking my pipe. I sincerely hope that it does not read th= e entire reads-file into memory at any point, since I'm concerned that it'l= l start swapping if I load large data sets. Do you have any tips here to he= lp me out?

Best regards

Fredrik Boulund 
-- =0A=
=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=
=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=
=0A=
Fredrik Boulund, PhD student=0A=
Department of Mathematical Sciences=0A=
Division of Mathematical Statistics=0A=
Chalmers University of Technology, =0A=
SE-412 96 Gothenburg, Sweden=0A=
Email: fredrik.boulund@chalmers.se =0A=
Phone: +46(0)31-772-5342, mobile +46(0)73-770 6629=0A=
=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=
=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=97=
=0A=
--_000_FCCAB9D80C3DAB47B5601C5B0E62872B19A66B9Dex02acampusfube_-- From manuel.holtgrewe@fu-berlin.de Wed Nov 14 22:24:25 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TYkRc-004A4W-Ay>; Wed, 14 Nov 2012 22:24:24 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TYkRc-0044Wj-8U>; Wed, 14 Nov 2012 22:24:24 +0100 Received: from cas1.campus.fu-berlin.de ([130.133.170.201]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TYkRb-000Dis-TM>; Wed, 14 Nov 2012 22:24:24 +0100 Received: from EX02A.campus.fu-berlin.de ([130.133.170.132]) by CAS1.campus.fu-berlin.de ([130.133.170.201]) with mapi id 14.02.0318.004; Wed, 14 Nov 2012 22:24:22 +0100 From: "Holtgrewe, Manuel" To: SeqAn Development Thread-Topic: [Seqan-dev] Some SeqAn problems Thread-Index: AQHNt9FmXsMqjk/ls0+cblS4r6nZWpfp7F52 Message-ID: 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_FCCAB9D80C3DAB47B5601C5B0E62872B19A66BADex02acampusfube_" MIME-Version: 1.0 Date: Wed, 14 Nov 2012 22:24:21 +0100 X-Original-Date: Wed, 14 Nov 2012 21:24:21 +0000 X-Originating-IP: 130.133.170.201 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1352928264-0000097C-3F8B9A5E/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED,HTML_MESSAGE X-Spam-Checker-Version: SpamAssassin 3.3.2 on Algerien.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Some SeqAn problems X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 14 Nov 2012 21:24:25 -0000 --_000_FCCAB9D80C3DAB47B5601C5B0E62872B19A66BADex02acampusfube_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Jose, I think this is a problem with the MacPorts install. We are planning to publish some improvements of the build system such that = it will be easier to keep the MacPorts builds up to date. For now, may I ask you to do a SVN checkout of http://svn.seqan.de/seqan/tr= unk/ and use the include headers from there? It should be enough to check o= ut the core/include and extras/include folders and make both available in y= our include path. Please report any further problems to this list. I will get back to you in = a more timely fashion than with this email. Sorry for any inconvenience, Manuel ________________________________ From: Jos=E9 Iguelmar Miranda [jose.ig.miranda@gmail.com] Sent: Thursday, November 01, 2012 2:36 AM To: seqan-dev@lists.fu-berlin.de Subject: [Seqan-dev] Some SeqAn problems Hi: First and foremost, my best congratulations for this wonderful C++ library.= SeqAn is an awesome contribution to sequence analysis. You guys are great! I installed SeqAn in my MBP-intel using MacPorts. Almost everything runs sm= ooth. But I am stuck with some problems: 1. In the tutorial PairwiseSequenceAlignment I got problems with the use of= LocalAlignmentEnumerator, Banded alignment (two last parms values) and glo= balAlignmentScore. The compiler error msg is "xxx was not declared in this = scope." Indeed, I double checked the headers and the ones corresponding to = these statements aren't available in the includes (/opt/local/include/seqan= /). 2. The same happens with FMIndex (was not declared in this scope). 3. In the graph tutorial, the same happens with assignVertexMap (was not de= clared in this scope). Searching your sources, I could find the headers for these statements. Woul= d it be a problem with the MacPorts installation? Best regards. Jose I Miranda. --_000_FCCAB9D80C3DAB47B5601C5B0E62872B19A66BADex02acampusfube_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Jose,

I think this is a problem with the MacPorts install.

We are planning to publish some improvements of the build system such = that it will be easier to keep the MacPorts builds up to date.

For now, may I ask you to do a SVN checkout of http://svn.seqan.de/seqan/trun= k/ and use the include headers from there? It should be enough to = check out the core/include and extras/include folders and make both available in your include path.

Please report any further problems to this list. I will get back to yo= u in a more timely fashion than with this email.

Sorry for any inconvenience,
Manuel

From: Jos=E9 Iguelmar Miranda [jose.ig.mi= randa@gmail.com]
Sent: Thursday, November 01, 2012 2:36 AM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Some SeqAn problems

Hi:

First and foremost, my best congratulations for this wonderful C+&= #43; library. SeqAn is an awesome contribution to sequence analysis. You gu= ys are great!

I installed SeqAn in my MBP-intel using MacPorts. Almost everything ru= ns smooth. But I am stuck with some problems:

1. In the tutorial PairwiseSequenceAlignment I got problems with the u= se of LocalAlignmentEnumerator, Banded alignment (two last parms values) an= d globalAlignmentScore. The compiler error msg is "xxx was not declare= d in this scope." Indeed, I double checked the headers and the ones corresponding to these statements aren't availabl= e in the includes (/opt/local/include/seqan/).

2. The same happens with FMIndex (was not declared in this scope)= .

3. In the graph tutorial, the same happens with assignVertexMap (was n= ot declared in this scope).

Searching your sources, I could find the headers for these statements.= Would it be a problem with the MacPorts installation?

Best regards.
Jose I Miranda.

--_000_FCCAB9D80C3DAB47B5601C5B0E62872B19A66BADex02acampusfube_-- From jose.ig.miranda@gmail.com Thu Nov 15 01:06:05 2012 Received: from relay1.zedat.fu-berlin.de ([130.133.4.67]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TYmy4-000Bmk-Sl>; Thu, 15 Nov 2012 01:06:04 +0100 Received: from mail-la0-f54.google.com ([209.85.215.54]) by relay1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1TYmy4-003joS-Q4>; Thu, 15 Nov 2012 01:06:04 +0100 Received: by mail-la0-f54.google.com with SMTP id j13so1054547lah.13 for ; Wed, 14 Nov 2012 16:06:03 -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=1DwHzOSfpBXA2EnynhykOQ4J4S0myyiPcOCdvePTHAQ=; b=SpG8934Vp1gXTgMudWbkQ+arTnWO0iUINgJXv076Q2xW4Nfb5Foph91tNE2j4i6Ls8 2hfhv/bSBmju7tfHBRzR+Vqu82H3GrUtgWlzPyl4SYejisbr7fLSL214XB7MQryWSr+7 qRRXZvNXvd7uvnCFKIgNbmhEH8BpFHCcvHHqGeyctBAGBODDRKFy0OFF4S4+CrMhAHUZ TsqgouIXdnSUNg8y1QFiWGMOaimy7BwamVW8ccgznCnI1H/Dq5fBkvVoIfqIlUM5nVO4 iO9Sl4XAC5GayEMMqyJLXn4Vs0XVAa2rWaaTdRCbk5aghE5Sz1idlYhy9imsHdil4b4t 3vDw== MIME-Version: 1.0 Received: by 10.152.106.162 with SMTP id gv2mr26175928lab.14.1352937963312; Wed, 14 Nov 2012 16:06:03 -0800 (PST) Received: by 10.114.5.225 with HTTP; Wed, 14 Nov 2012 16:06:03 -0800 (PST) In-Reply-To: References: Date: Wed, 14 Nov 2012 22:06:03 -0200 Message-ID: From: =?ISO-8859-1?Q?Jos=E9_Iguelmar_Miranda?= To: SeqAn Development Content-Type: multipart/alternative; boundary=f46d04083aa5b4d4ea04ce7d6a02 X-Originating-IP: 209.85.215.54 X-ZEDAT-Hint: A X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1352937964-0000097C-CF9804BF/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.000000, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-0.7 required=5.0 tests=FREEMAIL_FROM,HTML_MESSAGE, RCVD_IN_DNSWL_LOW,T_DKIM_INVALID X-Spam-Checker-Version: SpamAssassin 3.3.2 on Benin.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: Re: [Seqan-dev] Some SeqAn problems X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 15 Nov 2012 00:06:05 -0000 --f46d04083aa5b4d4ea04ce7d6a02 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Manuel: I supposed so, too. Meanwhile, I am using the "make" version. Everything is going well. I was waiting for the return of Jochen (14/11) to tell him that I am using SeqAn in full. Thank you guys for your attentive support. SeqAn is really good and I'm learning a lot on bioinformatics with it. I wish SeqAn long life and becoming better even more. Cheers. Jos=E9. On Wed, Nov 14, 2012 at 7:24 PM, Holtgrewe, Manuel < manuel.holtgrewe@fu-berlin.de> wrote: > Dear Jose, > > --f46d04083aa5b4d4ea04ce7d6a02 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Manuel:

I supposed so, too.
Meanwhile, I am= using the "make" version. Everything is going well.
I = was waiting for the return of Jochen (14/11) to tell him that I am using Se= qAn in full.
Thank you guys for your attentive support.
SeqAn is really g= ood and I'm learning a lot on bioinformatics with it.
I wish = SeqAn long life and becoming better even more.

Cheers.
Jos=E9.

On Wed, Nov 14,= 2012 at 7:24 PM, Holtgrewe, Manuel <manuel.holtgrewe@fu-berli= n.de> wrote:
Dear Jose,

--f46d04083aa5b4d4ea04ce7d6a02-- From manuel.holtgrewe@fu-berlin.de Thu Nov 29 15:38:41 2012 Received: from outpost1.zedat.fu-berlin.de ([130.133.4.66]) by list1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Te5GC-000Q2V-DC>; Thu, 29 Nov 2012 15:38:40 +0100 Received: from relay2.zedat.fu-berlin.de ([130.133.4.80]) by outpost1.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Te5GC-001bJI-Bq>; Thu, 29 Nov 2012 15:38:40 +0100 Received: from cas3.campus.fu-berlin.de ([130.133.170.203]) by relay2.zedat.fu-berlin.de (Exim 4.69) for seqan-dev@lists.fu-berlin.de with esmtp (envelope-from ) id <1Te5GB-003aDW-Ty>; Thu, 29 Nov 2012 15:38:40 +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 14.02.0318.004; Thu, 29 Nov 2012 15:38:39 +0100 From: "Holtgrewe, Manuel" To: =?windows-1256?Q?SeqAn_Development_=FD=5Bseqan-dev=40lists=2Efu-berlin=2E?= =?windows-1256?Q?de=5D=FD?= Thread-Topic: SeqAn Build System Rewrite Thread-Index: Ac3OPfwTcvKIRCnjTPytbCGdyXr2kA== Message-ID: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: Content-Type: text/plain; charset="windows-1256" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Date: Thu, 29 Nov 2012 15:38:37 +0100 X-Original-Date: Thu, 29 Nov 2012 14:38:37 +0000 X-Originating-IP: 130.133.170.203 X-purgate: clean X-purgate-type: clean X-purgate-ID: 151147::1354199920-0000097C-CCE80449/0-0/0-0 X-Bogosity: Ham, tests=bogofilter, spamicity=0.001680, version=1.2.2 X-Spam-Flag: NO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED X-Spam-Checker-Version: SpamAssassin 3.3.2 on Botsuana.ZEDAT.FU-Berlin.DE X-Spam-Level: Subject: [Seqan-dev] SeqAn Build System Rewrite X-BeenThere: seqan-dev@lists.fu-berlin.de X-Mailman-Version: 2.1.14 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, 29 Nov 2012 14:38:41 -0000 Dear all,=0A= =0A= I have just committed an update to the SeqAn build system. The main visible= changes are that the Release mode is now the default CMAKE_BUILD_TYPE such= that people who just want to build a SeqAn application do not accidently b= uild the debug version any more and that the binaries are now all copied to= "bin/" in the build directory.=0A= =0A= Other major changes are:=0A= =0A= * The FindSeqAn.cmake module is now a real CMake module. This means you can= use "find_package(SeqAn)" in your own CMake projects outside the SeqAn bui= ld system. You only have to copy over the file utils/cmake/FindSeqAn.cmake.= =0A= =0A= * It is now possible to generate project files/build systems for one applic= ation only. This makes it easier for us to release applications for multipl= e platforms and plays together nicely with our SVN restructuring.=0A= =0A= * The SeqAn apps now use the FindSeqAn.cmake module.=0A= =0A= The new system currently is backwards compatible with CMakeLists.txt files = from the previous version so you can take some time switching over the sand= box. However, the legacy functions are deprecated and their support will be= discontinued in the future.=0A= =0A= =0A= You can see how a plain sandbox with the new build system looks like by usi= ng the updated code generator:=0A= =0A= ./util/bin/skel.py repository sandbox/example=0A= ./util/bin/skel.py module ex_module sandbox/example=0A= ./util/bin/skel.py test ex_module sandbox/example=0A= ./util/bin/skel.py app ex_app sandbox/example=0A= ./util/bin/skel.py demo ex_demo sandbox/example=0A= =0A= =0A= There is documentation on the new build system in the SeqAn Wiki:=0A= =0A= http://trac.seqan.de/wiki/BuildManual=0A= =0A= I hope this causes not too much inconvenience for you. If there is any prob= lem for you then please report it to us and we will help you fix it.=0A= =0A= Cheers,=0A= Manuel=