| Previous changeset 27:8be4f23d1018 (2015-03-30) Next changeset 29:ce2bb7841f17 (2015-04-07) |
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Commit message:
Update to most recent GitHub version passing tests. |
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modified:
bam_dump.xml fastq_dump.xml sam_dump.xml sra_pileup.xml |
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added:
LICENSE README.md test-data/bam_dump_result.bam test-data/sam_dump_result.sam test-data/sra_pileup_result.pileup |
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removed:
README.txt |
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| diff -r 8be4f23d1018 -r fdc981664a43 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Wed Apr 01 12:35:38 2015 -0400 |
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| @@ -0,0 +1,60 @@ +CONTENTS + + Public Domain Notice + Exceptions (for bundled 3rd-party code) + Copyright F.A.Q. + + +============================================================== + PUBLIC DOMAIN NOTICE + National Center for Biotechnology Information + +With the exception of certain third-party files summarized below, this +software is a "United States Government Work" under the terms of the +United States Copyright Act. It was written as part of the authors' +official duties as United States Government employees and thus cannot +be copyrighted. This software is freely available to the public for +use. The National Library of Medicine and the U.S. Government have not +placed any restriction on its use or reproduction. + +Although all reasonable efforts have been taken to ensure the accuracy +and reliability of the software and data, the NLM and the U.S. +Government do not and cannot warrant the performance or results that +may be obtained by using this software or data. The NLM and the U.S. +Government disclaim all warranties, express or implied, including +warranties of performance, merchantability or fitness for any +particular purpose. + +Please cite the authors in any work or product based on this material. + + +============================================================== +Copyright F.A.Q. + + +-------------------------------------------------------------- +Q. Our product makes use of the NCBI source code, and we made changes + and additions to that version of the NCBI code to better fit it to + our needs. Can we copyright the code, and how? + +A. You can copyright only the *changes* or the *additions* you made to the + NCBI source code. You should identify unambiguously those sections of + the code that were modified, e.g. by commenting any changes you made + in the code you distribute. Therefore, your license has to make clear + to users that your product is a combination of code that is public domain + within the U.S. (but may be subject to copyright by the U.S. in foreign + countries) and code that has been created or modified by you. + +-------------------------------------------------------------- +Q. Can we (re)license all or part of the NCBI source code? + +A. No, you cannot license or relicense the source code written by NCBI + since you cannot claim any copyright in the software that was developed + at NCBI as a 'government work' and consequently is in the public domain + within the U.S. + +-------------------------------------------------------------- +Q. What if these copyright guidelines are not clear enough or are not + applicable to my particular case? + +A. Contact us. Send your questions to 'sra-tools@ncbi.nlm.nih.gov'. |
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| diff -r 8be4f23d1018 -r fdc981664a43 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Apr 01 12:35:38 2015 -0400 |
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| @@ -0,0 +1,30 @@ +[](https://travis-ci.org/mdshw5/sra-tools-galaxy) + +The Galaxy tool wrappers contained in this tool shed repository rely on software developed by +the NCBI: http://github.com/ncbi/sra-tools. + +# INSTALLATION + +This software release was designed to install using the Galaxy toolshed under Linux and MacOS operating systems on Intel x86-compatible 32/64 bit architectures. + +*Build Requirements* + +- bash +- git +- make +- gcc +- g++ +- perl +- libxml2 + +On a Debian OS use: + + apt-get install build-essential libxml2-dev git + +On a Mac with [command line tools](https://developer.apple.com/downloads/index.action) installed: + + brew install git libxml2 + +CONTROLLED-ACCESS DATA + +Encrypted, controlled-access data is not supported. |
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| diff -r 8be4f23d1018 -r fdc981664a43 README.txt --- a/README.txt Mon Mar 30 22:40:59 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,39 +0,0 @@ -The Galaxy tool wrappers contained in this tool shed repository rely on software developed by -the NCBI Sequence Read Archive: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. -Use of SRA Toolkit software herin should comply with the GPL v2 or greater. - -Copyright (C) 2013 Matthew Shirley - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 2 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. - -INSTALLATION - -This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. - -Build Requirements: - ar - bash - make - gcc, g++ - libxml2 - libcurl4 - zlib - -On a debian based Linux OS use: - - apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev - -CONTROLLED-ACCESS DATA - -Encrypted, controlled-access data is not supported in this version of the SRA Toolkit Galaxy tool shed. \ No newline at end of file |
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| diff -r 8be4f23d1018 -r fdc981664a43 bam_dump.xml --- a/bam_dump.xml Mon Mar 30 22:40:59 2015 -0400 +++ b/bam_dump.xml Wed Apr 01 12:35:38 2015 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="bam_dump" name="Extract reads" version="1.1.2"> <description> in BAM format from NCBI SRA.</description> <command> - sam-dump --log-level fatal + sam-dump --log-level fatal --disable-multithreading #if str( $region ) != "": --aligned-region $region #end if @@ -11,7 +11,7 @@ #if str( $minMapq ) != "": --minmapq $minMapq #end if - #if $header == "yes": + #if str( $header ) == "yes": --header #else: --no-header @@ -29,10 +29,8 @@ $input.file #elif $input.input_select == "accession_number": $input.accession - #elif $input.input_select == "text": - `cat $input.text` #end if - | samtools view -Sb - > $output + | samtools view -Sb - 2> /dev/null > $output </command> <version_string>sam-dump --version</version_string> <inputs> @@ -40,7 +38,6 @@ <param name="input_select" type="select" label="select input type"> <option value="accession_number">SRR accession</option> <option value="file">SRA archive in current history</option> - <option value="text">text file containing SRR accession</option> </param> <when value="file"> <param format="sra" name="file" type="data" label="sra archive"/> @@ -48,12 +45,9 @@ <when value="accession_number"> <param format="text" name="accession" type="text" label="accession"/> </when> - <when value="text"> - <param format="txt" name="text" type="data" label="text file"/> - </when> </conditional> - <param format="text" name="region" type="text" label="aligned region"/> - <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/> + <param format="text" name="region" type="text" label="aligned region (chr:start-end)"/> + <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to)"/> <param format="text" name="header" type="select" value="yes"> <label>output BAM header</label> <option value="yes">Yes</option> @@ -75,14 +69,25 @@ <outputs> <data name="output" format="bam"/> </outputs> + <stdio> + <exit_code range="127" level="fatal" description="Could not locate sam-dump and/or samtools binary"/> + </stdio> <requirements> <requirement type="package" version="2.4.5">sra_toolkit</requirement> <requirement type="package" version="1.2">samtools</requirement> </requirements> + <tests> + <test> + <param name="input_select" value="accession_number"/> + <param name="accession" value="SRR925743"/> + <param name="region" value="17:41243452-41277500"/> + <output name="output" file="bam_dump_result.bam" ftype="bam" /> + </test> + </tests> <help> - This tool extracts reads from sra archives using sam-dump. - Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. - The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. - Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. + This tool extracts reads from sra archives using sam-dump. + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. + The sam-dump program is developed at NCBI, and is available at: http://github.com/ncbi/sra-tools + Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy. </help> </tool> |
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| diff -r 8be4f23d1018 -r fdc981664a43 fastq_dump.xml --- a/fastq_dump.xml Mon Mar 30 22:40:59 2015 -0400 +++ b/fastq_dump.xml Wed Apr 01 12:35:38 2015 -0400 |
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| @@ -1,5 +1,5 @@ <tool id="fastq_dump" name="Extract reads" version="1.1.2"> - <description> from NCBI SRA.</description> + <description> in FASTQ/A format from NCBI SRA.</description> <command> fastq-dump --log-level fatal #if $input.input_select == "file": @@ -123,9 +123,9 @@ </test> </tests> <help> - This tool extracts reads from SRA archives using fastq-dump. - Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. - The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. - Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. + This tool extracts reads from sra archives using sam-dump. + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. + The sam-dump program is developed at NCBI, and is available at: http://github.com/ncbi/sra-tools + Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy. </help> </tool> |
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| diff -r 8be4f23d1018 -r fdc981664a43 sam_dump.xml --- a/sam_dump.xml Mon Mar 30 22:40:59 2015 -0400 +++ b/sam_dump.xml Wed Apr 01 12:35:38 2015 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="sam_dump" name="Extract reads" version="1.1.2"> <description> in SAM format from NCBI SRA.</description> <command> - sam-dump --log-level fatal + sam-dump --log-level fatal --disable-multithreading #if str( $region ) != "": --aligned-region $region #end if @@ -11,7 +11,7 @@ #if str( $minMapq ) != "": --minmapq $minMapq #end if - #if $header == "yes": + #if str( $header ) == "yes": --header #else: --no-header @@ -25,15 +25,10 @@ #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ): --primary #end if - #if str( $fastq ) == "yes": - --fastq - #end if #if $input.input_select == "file": $input.file #elif $input.input_select == "accession_number": $input.accession - #elif $input.input_select == "text": - `cat $input.text` #end if > $output </command> @@ -43,7 +38,6 @@ <param name="input_select" type="select" label="select input type"> <option value="accession_number">SRR accession</option> <option value="file">SRA archive in current history</option> - <option value="text">text file containing SRR accession</option> </param> <when value="file"> <param format="sra" name="file" type="data" label="sra archive"/> @@ -51,12 +45,9 @@ <when value="accession_number"> <param format="text" name="accession" type="text" label="accession"/> </when> - <when value="text"> - <param format="txt" name="text" type="data" label="text file"/> - </when> </conditional> - <param format="text" name="region" type="text" label="aligned region"/> - <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/> + <param format="text" name="region" type="text" label="aligned region (chr:start-end)"/> + <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to)"/> <param format="text" name="header" type="select" value="yes"> <label>output SAM header</label> <option value="yes">Yes</option> @@ -74,26 +65,25 @@ <option value="yes">Yes</option> </param> <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> - <param format="text" name="fastq" type="select" value="no"> - <label>output fastq</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> </inputs> <outputs> - <data name="output" format="sam"> - <change_format> - <when input="fastq" value="yes" format="fastq"/> - </change_format> - </data> + <data name="output" format="sam"/> </outputs> <requirements> <requirement type="package" version="2.4.5">sra_toolkit</requirement> </requirements> + <tests> + <test> + <param name="input_select" value="accession_number"/> + <param name="accession" value="SRR925743"/> + <param name="region" value="17:41243452-41277500"/> + <output name="output" file="sam_dump_result.sam" ftype="sam" /> + </test> + </tests> <help> - This tool extracts reads from sra archives using sam-dump. - Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. - The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. - Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. + This tool extracts reads from sra archives using sam-dump. + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. + The sam-dump program is developed at NCBI, and is available at: http://github.com/ncbi/sra-tools + Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy. </help> </tool> |
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| diff -r 8be4f23d1018 -r fdc981664a43 sra_pileup.xml --- a/sra_pileup.xml Mon Mar 30 22:40:59 2015 -0400 +++ b/sra_pileup.xml Wed Apr 01 12:35:38 2015 -0400 |
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| @@ -42,10 +42,18 @@ <requirements> <requirement type="package" version="2.4.5">sra_toolkit</requirement> </requirements> + <tests> + <test> + <param name="input_select" value="accession_number"/> + <param name="accession" value="SRR925743"/> + <param name="region" value="17:41243452-41277500"/> + <output name="output" file="sra_pileup_result.pileup" ftype="pileup" /> + </test> + </tests> <help> - This tool produces pileup format from sra archives using sra-pileup. - Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. - The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. - Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. + This tool extracts reads from sra archives using sam-dump. + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. + The sam-dump program is developed at NCBI, and is available at: http://github.com/ncbi/sra-tools + Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy. </help> </tool> |
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| diff -r 8be4f23d1018 -r fdc981664a43 test-data/bam_dump_result.bam |
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| Binary file test-data/bam_dump_result.bam has changed |
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| diff -r 8be4f23d1018 -r fdc981664a43 test-data/sam_dump_result.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sam_dump_result.sam Wed Apr 01 12:35:38 2015 -0400 |
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GGTCAATTCTGTTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATTCCTATGA\tHHHHHGHHHFHHHHHHHGFHHHHHHHHHHHHFBHHHHHHEHHHHHHF>DHHFHHFHHHHHFHCHFHGGHHHHHFHHFF;HBFFD?GFDFAACCAFEEFE?\tRG:Z:0\n+44155503\t133\t*\t0\t0\t*\t17\t41275955\t0\tTATGTAAGGTCAATTCTGTTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATTCCTATGA\tHHHHHHHHHBFFFFGFHFFHEHGHGGFEFFFHFEF@EFEEHHHHFHFHDHFHHHHHHFHEHHHHFHHHHHHHHFBE:FAAFEFEFHDHHBCE?FF>ADA5\tRG:Z:0\n+44155504\t133\t*\t0\t0\t*\t17\t41275955\t0\tTATGTAAGGTCAATTCTGTTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATTCCTATGA\tHHHHHGHHH:HHHHHHHH<HGFFGGHEHHHHHHHHHHHFHHHHHFHDGDHGGFGGHHHHHHHHHHFHHHBGF?IA@5A>B6;>??FGFA4>ACB5ECEE#\tRG:Z:0\n+44155505\t133\t*\t0\t0\t*\t17\t41275976\t0\tATTTGCATAGGAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATTCCTATGATTATCTCCTATGCAAATAGATCG\tHHHHHHHHHFHHHHHHHHHHHHHHGFHFHHHHHHHHHFHHHHHHHHHHHFIGECIEIGGGHHHHHHGHHHHHFHGHHHHHHHHHHHHFEHFDDFFFFFCG\tRG:Z:0\n+44155511\t165\t*\t0\t0\t*\t17\t41275978\t0\tCATTAATGCTATGCAGATAATCATAGGAATCCCAAATTAATACACTCTTGTGCTGACTTACCAGATGGGACACTCTAAGATTTTCTGCATAGCATTAATG\tHHHHHHHHHHHHHHHHHGHDHHHHHHHHHHHHHEHHHHHHHGHHHGHHHHHHHHHHHHHHHHHHHGFHHFHHHHHFHEBGHHHHHD<EFGBBBCAGFGE;\tRG:Z:0\n+44155516\t165\t*\t0\t0\t*\t17\t41275988\t0\tCATTAATGCTATGCAGATAATCATAGGAATCCCAAATTAATACACTCTTGTGCTGACTTACCAGATGGGACACTCTAAGATTTTCTGCATAGCATTAATG\tHHHHHHHHHHHHHHHHFGHHHHHHGHHHHHHHHGHFHHHHHHHEHHHHHFHHHHHFHHHHHHHHHFCCDDHFFHGFHHHBBHFHHFFF@FEFCCBBEE=:\tRG:Z:0\n+44155520\t133\t*\t0\t0\t*\t17\t41276001\t0\tATCCCAAATTAATACACTCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGG\tHHHHHHHHHHHHHHHHHHHHHGHFHDHFHFHHHHHHHFHBHEHHFHHHHHGGGBGEHGGIHHHHHDHEHHEHHHHBHHHHHFFFFFEHEECHEBDEFEF#\tRG:Z:0\n+44155522\t133\t*\t0\t0\t*\t17\t41276005\t0\tCAAATTAATACACTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTA\tHHHHHHHHHHHGHHHGHHHHGHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHFHEHGHHHHGHHHBHEHFHHHEF3FF######\tRG:Z:0\n+44155523\t133\t*\t0\t0\t*\t17\t41276005\t0\tCAAATTAATACACTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTA\tFGDBGEFFDGGDEFGFFGFG=EACE>CBDDFCFBBDBCCDEGGFEEEE=ECADDFFGD@BGFFEEC8EEE=EEGDBDDDEGBDFG7@B>BAGBADGDEEB\tRG:Z:0\n+44155531\t165\t*\t0\t0\t*\t17\t41276036\t0\tAAGTTCATTGGGACACTCTAAGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTCCAAT\tHFHHEHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHACFIFGIGHHHFHFGHHHHHFHHFF5HH\tRG:Z:0\n+44155532\t165\t*\t0\t0\t*\t17\t41276056\t0\tAGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT\tHHHHHHHHHHHHHHHHHGHHHHHHHHHHHFHHHHHHGHHHHFGHHGHHHHHHHHHHHHHHHEHHFGBGGGFHHHHHHDHHHHHHFGHHC:EA9BEEDDGB\tRG:Z:0\n+44155533\t165\t*\t0\t0\t*\t17\t41276058\t0\tAGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT\tHHHHHHHHHHHHHHHHHHHHHHDEHEHHHHEHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHGHEHHEHHHHHHHHHHHHEHHHHHFHHFHHHEEHF9\tRG:Z:0\n+44155535\t165\t*\t0\t0\t*\t17\t41276061\t0\tAGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT\tHHHHHHFHHHHHHHHHHHHGHHHFHHHHHFHHHHHFHHHHHHHHHHFHHHGFHHFGHHHHHHHHHEFHHHHHGHHGGHHGHHHHEGH=CHG@E<G@CEA?\tRG:Z:0\n+44155536\t165\t*\t0\t0\t*\t17\t41276063\t0\tAACAGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTAGATCGGAAGAG\tHHHHHHHHHFHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHFHHHHEHEHHHEHGHHHFEHFHHHHHHHHHFHEHHGHFHHHHFBFHHHHHF\tRG:Z:0\n' |
| b |
| diff -r 8be4f23d1018 -r fdc981664a43 test-data/sra_pileup_result.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sra_pileup_result.pileup Wed Apr 01 12:35:38 2015 -0400 |
| b |
| b'@@ -0,0 +1,7349 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