# HG changeset patch
# User jasmine_amir
# Date 1675379465 18000
# Node ID 878e5d4becef34323440b260feb56e924bf39f5a
planemo upload
diff -r 000000000000 -r 878e5d4becef LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Thu Feb 02 18:11:05 2023 -0500
@@ -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'.
diff -r 000000000000 -r 878e5d4becef README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,32 @@
+The Galaxy tool wrappers contained in this tool shed repository rely on software developed by
+the NCBI: https://github.com/ncbi/sra-tools.
+
+NCBI Sequence Read Archive Toolkit: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
+
+# Installation of Aspera connect ascp binary
+
+The sra-tools suite is ready to benefit from increased transfer speed and reliability by using Aspera Connect ascp.
+To benefit, download the ascp commandline client, and place ascp and the required ssh keys into a PATH accessible to galaxys job handler.
+
+A convenience package for linux and OS X is available at https://toolshed.g2.bx.psu.edu/view/mvdbeek/package_ascp_3/e109f0ec22c3 .
+It suffices to copy the contents of the $INSTALL_DIR/bin into PATH.
+
+Alternatively go to http://downloads.asperasoft.com/connect2/ .
+
+Aspera connect is not provided by the IUC due to its closed-source nature.
+
+# Firewall settings for highspeed transfer
+
+To benefit from increased transfer speeds using ascp3 your local firewall must permit UDP data transfer in both
+directions on ports 33001-33009 for the following IP ranges:
+
+ 130.14.*.*
+
+ 165.112.*.*
+
+The firewall must also allow ssh traffic outbound to NCBI.
+The wrapper will fall back to http download if these requirements are not met.
+
+CONTROLLED-ACCESS DATA
+
+Encrypted, controlled-access data is not supported.
diff -r 000000000000 -r 878e5d4becef fasterq_dump.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fasterq_dump.xml Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,231 @@
+
+ format from NCBI SRA
+
+ macros.xml
+
+
+
+
+ fasterq-dump --version | tr -d $'\n'
+ &1 | tee -a '$log';
+ if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then
+ break ;
+ else
+ echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ;
+ SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ;
+ sleep 1 ;
+ fi ;
+ done &&
+ mkdir -p output &&
+ mkdir -p outputOther &&
+ count="\$(ls *.fastq | wc -l)" &&
+ echo "There are \$count fastq files" &&
+ data=(\$(ls *.fastq)) &&
+ if [ "\$count" -eq 1 ]; then
+ @COMPRESS@ "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz &&
+ rm "\${data[0]}";
+ elif [ "$adv.split" = "--split-3" ]; then
+ if [ -e "\${acc}".fastq ]; then
+ @COMPRESS@ "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz;
+ fi &&
+ @COMPRESS@ "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
+ @COMPRESS@ "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
+ rm "\${acc}"*.fastq;
+ elif [ "\$count" -eq 2 ]; then
+ #if $adv.skip_technical:
+ @COMPRESS@ "\${data[0]}" > output/"\${acc}"_forward.fastqsanger.gz &&
+ @COMPRESS@ "\${data[1]}" > output/"\${acc}"_reverse.fastqsanger.gz &&
+ #else
+ @COMPRESS@ "\${data[0]}" > outputOther/"\${data[0]}"sanger.gz &&
+ @COMPRESS@ "\${data[1]}" > outputOther/"\${data[1]}"sanger.gz &&
+ #end if
+ rm "\${data[0]}" &&
+ rm "\${data[1]}";
+ else
+ for file in \${data[*]}; do
+ @COMPRESS@ "\$file" > outputOther/"\$file"sanger.gz &&
+ rm "\$file";
+ done;
+ fi;
+
+ #if $input.input_select != "sra_file":
+ ); done;
+ #end if
+ echo "Done with all accessions."
+ ]]>
+
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diff -r 000000000000 -r 878e5d4becef fastq_dump.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_dump.xml Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,270 @@
+
+ format from NCBI SRA
+
+ macros.xml
+
+
+
+
+ fastq-dump --version | tr -d $'\n'
+
+
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diff -r 000000000000 -r 878e5d4becef macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,188 @@
+
+ 3.0.0
+ 0
+ 21.09
+
+
+ topic_0622
+ topic_0091
+
+
+ operation_2422
+ operation_0335
+
+
+
+
+ sra-tools
+ pigz
+ samtools
+
+
+
+
+ grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
+
+
+
+
+
+ sra-tools
+
+
+
+ accessions &&
+ #else
+ @ACCESSIONS_FROM_FILE@ '$input.file_list' > accessions &&
+ #end if
+ #elif $input.input_select == "accession_number":
+ echo '${input.accession}' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions &&
+ #end if
+ for acc in \$(cat ./accessions);
+ do (
+ echo "Downloading accession: \$acc..." &&
+ #end if
+ ]]>
+
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+ 10.1093/nar/gkq1019
+
+@misc{github_sratools,
+ author = {NCBI},
+ title = {sra-tools},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/ncbi/sra-tools},
+}
+
+
+
+ **How to use it?**
+
+There are three ways in which you can download data:
+
+ 1. Plain text input of accession number(s)
+ 2. Providing a list of accessions from file
+ 3. Extracting data from an already uploaded SRA dataset
+
+Below we discuss each in detail.
+
+------
+
+**Plain text input of accession number(s)**
+
+When you type an accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch the data for you. You can also provide a list of multiple accession numbers (e.g. `SRR3141592, SRR271828, SRR112358`).
+
+-----
+
+**Providing a list of accessions from file**
+
+A more realistic scenario is when you want to upload a number of datasets at once. To do this you need a list of accession, where there is only one accession per line (see below for information on how to generate such a file). Once you have this file:
+
+ 1. Upload it into your history using Galaxy's upload tool
+ 2. Once the list of accessions is uploaded choose *List of SRA accessions, one per line* from **select input type** dropdown
+ 3. Choose uploaded file within the **sra accession list** field
+ 4. Click **Execute**
+
+-----
+
+**Extract data from an already uploaded SRA dataset**
+
+If an SRA dataset is already present in the history, the sequencing data can be extracted in a human-readable data format (fastq, sam, bam) by setting **select input type** drop-down to *SRA archive in current history*.
+
+
+-----
+
+**How to generate accession lists**
+
+ 1. Go to **SRA Run Selector** by clicking this link_
+ 2. Find the study you are interested in by typing a search term within the **Search** box. This can be a word (e.g., *mitochondria*) or an accession you have gotten from a paper (e.g., *SRR1582967*).
+ 3. Once you click on the study of interest you will see the number of datasets in this study within the **Related SRA data** box
+ 4. Click on the Runs number
+ 5. On the page that would open you will see **Accession List** button
+ 6. Clicking of this button will produce a file that you will need to upload into Galaxy and use as the input to this tool.
+
+
+For credits, information, support and bug reports, please refer ato https://github.com/galaxyproject/tools-iuc.
+
+
diff -r 000000000000 -r 878e5d4becef sam_dump.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_dump.xml Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,127 @@
+
+ format from NCBI SRA
+
+ macros.xml
+
+
+
+
+ sam-dump --version | tr -d $'\n'
+ /dev/null > "\$acc.bam"
+ #elif str( $outputformat ) == "sam":
+ > "\$acc.sam"
+ #end if
+
+ #if $input.input_select != "sra_file":
+ ); done;
+ #end if
+ echo "Done with all accessions."
+ ]]>
+
+
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diff -r 000000000000 -r 878e5d4becef test-data/DRR015708_forward.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DRR015708_forward.fastqsanger Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,20 @@
+@HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/1
+NTATTGTAGCGCACTATGAGGTCGCTCATTANTNTACATCNNCATCCAAATTTCAGCATNANTTTNNNNNTGTTTGATATTCTCAAAGNGATNAACGTTT
++
+#1=DDFFFHGHHHJIIIIGIJFHIJJJJJJI#0#08DFII##-7@FHIIJJJJGEHEEE#,#,,;#####,,;?DCCDEFEEFCDDDD#+2+#+2C
+@HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/1
+NTAAAGGTTATTGTGCTTCACAGAAAATGCATTATTATGGGTATAAACTTCATGCGGTTTGCTCAGCGGAAGGTGTCTTTCAAAGTTTGGATATTAGTCC
++
+#1=DDFFEHHHHHGIJJJJGIJJJJJJJJJJJJIJJJJJJJCFGFIIHJIJHIJJJJHIJJJJIJIJIFHBDE;@ACEEEDDCCCCCDDDCCDCCFECCC
diff -r 000000000000 -r 878e5d4becef test-data/DRR015708_reverse.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DRR015708_reverse.fastqsanger Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,20 @@
+@HWI-ST895_0148_AC1GFWACXX:5:1101:1258:1938/2
+CATTANNAGNNANNNTTNNNNGANNNNNTCGANNNNNANTTTTAANCGNNNNNCTCTTNGAGAATATCAAANAGNTNAAAAATTANGCTGANNNTNGNAT
++
+CCCFF##4<##2###32####22#####11?F#####0#07CHGI#.;#####--;BB#,;?ADDDEEDDD#,8#,#,58C@C>CEC;A538:
+@HWI-ST895_0148_AC1GFWACXX:5:1101:2003:1864/2
+ATTGAAACCTTTTGAGTTGATTCGTGGATTTTTGATAAATGCATAATATCCTCTAAAAATTAAGGCATAAGCATCTAACAAAAAAAGTCTTTTATCTAAT
++
+CCCFFFFFHHHHHJEGGHIHIIJJHHJHIJIJJJGJIJJJJJJJJJJJJJIIIJIJJIJIJJIJJJJIGHEHIIHHHHFHFFEDDDDCDEEDDDDDDEDD
+@HWI-ST895_0148_AC1GFWACXX:5:1101:2399:1887/2
+TTGGTATTCTGCGGATAAATATCCTTTATCAGCTAAGAGCGTACAATTTTTAAACTGCTGTTTTATATCTTTCAGATAATGAATGTCATGCACTGAAGCT
++
+BCCFBDFFHHHHHJJJJJJJJJJJJJJJJJJJJJIJIFIJJHHIIIJJJJGHJJJJJJJJHIIJJIJJHHHHHHGEFFFFFFCDCEEEFDDDDCDD>CDD
diff -r 000000000000 -r 878e5d4becef test-data/ERR027433_forward.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ERR027433_forward.fastqsanger Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,20 @@
+@IL4_4847:5:1:1051:7109/1
+GCCGCCAACGTCCGACGGCGCGTCCCGCACGACTTGAACCGATCTCACCGAGACAGAACTAT
++
+C@CC@@@C2BBCBB:>@8@@5@>>@@@@@>@97@@==<@>>@4<'@8>:35=%&B#######
+@IL4_4847:5:1:1058:16093/1
+AAGGTCGGGCATTCGTTCGAGCCGACGACCGCGAGGAAGCGGTTCGGCCGGGCGTAGAATCC
++
+?ABBABB;<@>@=BCBB,,?):7@/3$54'818->1-+=+()$6--C8+?1
+@IL4_4847:5:1:1111:15034/1
+TCGATCCGCAGGGCAATCTGTGGATCCCGGCGTTCGACGACGGCGGGCGGGTGGCTCGGCAT
++
+2524;@@@/4<@6@;9?C@@93@>BAB2>>C@>B>C4BC4@-+B<@525++%=)########
+@IL4_4847:5:1:1122:6048/1
+ATCTCCTCGACGCGCACCAGATAGCGGTCGTAGCAATCGCCGTCCACGCCGACGGGCCCACT
++
+BBB@@@@@@@AB.<@2)7;B-@==:@>@@@A7@);9@@@@=1B@@@@2@=*:4@@@0%(-$,'3%%'%$%$,44%3&$=$C;CC-C##
diff -r 000000000000 -r 878e5d4becef test-data/ERR027433_reverse.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ERR027433_reverse.fastqsanger Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,20 @@
+@IL4_4847:5:1:1051:7109/3
+AACGCACTGCGCGCGGACTCGCCCCCGCGGCCACTCCGTGGGCCGGCGTACGGA
++
+)(664;(>>/:1<+/'())0)',8%'*7'+9904)'(+()'''':+4+'.7)'(
+@IL4_4847:5:1:1058:16093/3
+GCATAGCTGCCCTCGCCTTCTACTCGCACCGAACAAGCGGCCCGCCTACGCGGG
++
+;=>1(/2(:/=@(:'9/<(*'&.(?.6)(';+.5''-3.&''7(96%0:+($2$
+@IL4_4847:5:1:1111:15034/3
+GAGTGGAGCCGCGGACGGGAGCGCGGCGGCTGCCTCACAGCACCCGGGGGGTCG
++
+::3+:2655(*('((3*&&&4+')6'3/2,+++*.+')-/)4((<-+&&'&%<(
+@IL4_4847:5:1:1122:6048/3
+GAGGTCGGCGTTCTGGATGACAGGCGCGAAGCCCCCGCCGTCGGTGCCTTCACG
++
+=8+(-(,(3.5*=99+;).)8'(,(/(+(-6@'-3<6&,%/4++)')1/)>(.&
+@IL4_4847:5:1:1138:20693/3
+TGGACGTTGTGGTGGTTGTAAGAGATTTCGCTCCCCATGTTGGCGAGCTGCGAT
++
+;)?5;=9996@((((097:41=,A((+)5>9,:''''67+9)=(968-(8;8)3
diff -r 000000000000 -r 878e5d4becef test-data/ERR086330_1.fastq.gz
Binary file test-data/ERR086330_1.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/ERR086330_2.fastq.gz
Binary file test-data/ERR086330_2.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR002702_1.fastq.gz
Binary file test-data/SRR002702_1.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR002702_2.fastq.gz
Binary file test-data/SRR002702_2.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR11859153.fastq.gz
Binary file test-data/SRR11859153.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR11953971_1.fastq.gz
Binary file test-data/SRR11953971_1.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR11953971_2.fastq.gz
Binary file test-data/SRR11953971_2.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR1993644.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR1993644.fastqsanger Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,20 @@
+@1/2
+TATACTACTGTCATGTTTGCTTTTTTCGTGCTCATTACCTTATCGTATGCTTCCATCCAAAGATCTAGTTGTTTATAATATTCTCCCGGCCTTACTTCAAC
++
+?@GG48BBCF)8877=@=@C7=E??EBD:AADA;>C3;BB6:A@>>@:3>
+@2/2
+AAAAAAACTTTCTTTACAGGCGTAAAGAAAGTGAAATTGACAGTATTTATACATGAAATAGCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGAT
++
+<@@DA6DDF42ABGF9F?F@C04BGC>BFF>EBDBB@@:ACCCAB8@?=;B<@BABBBBB?#
+@3/2
+GTGCCATCATTTTCTATCCATTATTATGGATTATTGGCTCATCGTTTAATCCGGGTGATAGTTTATCTGGATCAAGTATTATTCCACAAAATGCAACGTTA
++
+=BBFFFFFHHHHHJJJJJJJJJJJJIJIJEIIGIJJJHGIGGIIGHIDIJGHIIJ?FFHGIIJJJJJJJJHGIHHHCEHFFFFFFFFEAECCDADDDDDDD
+@4/2
+TTCAAAACACATAAAGCTAATTGCCGCATATGACAATATTGCTAAAATAATTTTTTTACCAGATATCGGTGTTAATCGAAATAATGTACTTTCGGTCATTT
++
+BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJIIJJJJJJJIJJHHHHHFFDDCDEEEDDDDDDDDEDDDFFFEDDDDDDDDE
+@5/2
+ACTTGCCAATGCGATGCACCAATCTTTTCAGCAATAATCGGCAAAATTGGGTCGACTACTCCTATACCTGAAAAGGCAAGGAAAGTAGCCAACACTGTAAT
++
+BCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIIJIJHHHHFFFFFFEEEEEEDDDDDDDDDDDDDCDDDDDDDDDDDDDED
diff -r 000000000000 -r 878e5d4becef test-data/SRR522874.fastq.gz
Binary file test-data/SRR522874.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR522874.sra
Binary file test-data/SRR522874.sra has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR522874.sra_1.fastq.gz
Binary file test-data/SRR522874.sra_1.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR522874.sra_2.fastq.gz
Binary file test-data/SRR522874.sra_2.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR522874.sra_3.fastq.gz
Binary file test-data/SRR522874.sra_3.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR522874.sra_4.fastq.gz
Binary file test-data/SRR522874.sra_4.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR522874_1.fastq.gz
Binary file test-data/SRR522874_1.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR522874_2.fastq.gz
Binary file test-data/SRR522874_2.fastq.gz has changed
diff -r 000000000000 -r 878e5d4becef test-data/SRR522874_sam_dump_result.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR522874_sam_dump_result.sam Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,6 @@
+ETOOIVN07D9GPH 13 * 0 0 * * 0 0 GAATCCCGATATCATCATGAA 2L5AW?.A@BAB?A@ABBCN8
+ETOOIVN07D9GPH 141 * 0 0 * * 0 0 CATTGCTGAAAAACTCGGCGGCTGAGCGGGCTGGCAAGGC 8CN8=BC?]C7.%BA?I5?K7@>AA@AT@/A=K8BK8K7@
+ETOOIVN07ED00L 13 * 0 0 * * 0 0 ACTGAACACCACGAAGTAGA 5B@@G/:BN8A>AM6CCAA@
+ETOOIVN07ED00L 141 * 0 0 * * 0 0 AGTCGTACAGACGACGGTTGTCTGAGCGGGCTGGCAAGGC B7@A?CB>>ABB=BCM6N8==BBBA=AV@1=@K8AJ7K8A
+ETOOIVN07EE1GA 13 * 0 0 * * 0 0 GGAATTTTTCCGTTGCTGAT 7#K5]B7-$N8BM7BBCB>B
+ETOOIVN07EE1GA 141 * 0 0 * * 0 0 GCCAGGTGGACGTTAAATATCTGAGCGGGCTGGCAAGGC 9M7BK7AK4A>:N8Z@1BA8:>@:4+36945&4354445>/B>@
+@2/1
+AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGT
++
+HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFGGEEAEEEDD0ADDBD9BDBDDA@6?BA;?CD=:-7<<::)1;5,6-6A@?=9
+@3/1
+CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCA
++
+HHHHFHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHGEFHGEGGFGGGGGGHHHHEFEIDDEEEEEDD4DD;??:6>6<@.<==@?.@@@D@CD8->=>=<@CB@#####
+@5/1
+CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTCACACTCACCCTA
++
+GGGFGFFGGGFBGGEGGFFGGGCFFGGGGGEGFFFFFGFFGFFFDFFB+FGGFEE?FCF::7B5A?+BB###############################
diff -r 000000000000 -r 878e5d4becef test-data/SRR925743_reverse.fastqsanger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR925743_reverse.fastqsanger Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,20 @@
+@1/2
+CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
++
+GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF?EHGGHHHGHFHEHDEHGHFFEEE9BDDBEBAD.AD:ACBBC=4@>?5>=+?
+@2/2
+CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
++
+HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHHHHHHHHHHGHHHGHHBHGHHFDBDDED5FCFCEEGF<@>>>@,<5<@@?>;D
+@3/2
+ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT
++
+HHHHHHHHHFIEGFHFHDHHHHGFFHGEGDIGGEGGHHHAGEGGGDHHHHHHHHHHHFGDGGGEGDFFF>BEEEE3B;BB;>B7C@DA=DFBDD.BEE=9
+@4/2
+ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT
++
+GFFFHHFFHHHFHHFEFGGBGEEEE?<9?6=>>:=DDDD@DBGDB;DBDBA.ADD8<2<>6A@=A5>550=>>>>BE;EEEDEEE79+336<68=BCEB@
+@5/2
+ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGGTAGGGT
++
+479<.>><:+?=9@########
diff -r 000000000000 -r 878e5d4becef test-data/SRR925743_sam_dump_result.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRR925743_sam_dump_result.sam Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,10 @@
+44155511 165 * 0 0 * 17 41275978 0 CATTAATGCTATGCAGATAATCATAGGAATCCCAAATTAATACACTCTTGTGCTGACTTACCAGATGGGACACTCTAAGATTTTCTGCATAGCATTAATG HHHHHHHHHHHHHHHHHGHDHHHHHHHHHHHHHEHHHHHHHGHHHGHHHHHHHHHHHHHHHHHHHGFHHFHHHHHFHEBGHHHHHDCBDDFCFBBDBCCDEGGFEEEE=ECADDFFGD@BGFFEEC8EEE=EEGDBDDDEGBDFG7@B>BAGBADGDEEB RG:Z:0
+44155531 165 * 0 0 * 17 41276036 0 AAGTTCATTGGGACACTCTAAGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTCCAAT HFHHEHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHACFIFGIGHHHFHFGHHHHHFHHFF5HH RG:Z:0
+44155532 165 * 0 0 * 17 41276056 0 AGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT HHHHHHHHHHHHHHHHHGHHHHHHHHHHHFHHHHHHGHHHHFGHHGHHHHHHHHHHHHHHHEHHFGBGGGFHHHHHHDHHHHHHFGHHC:EA9BEEDDGB RG:Z:0
+44155533 165 * 0 0 * 17 41276058 0 AGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT HHHHHHHHHHHHHHHHHHHHHHDEHEHHHHEHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHGHEHHEHHHHHHHHHHHHEHHHHHFHHFHHHEEHF9 RG:Z:0
+44155535 165 * 0 0 * 17 41276061 0 AGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT HHHHHHFHHHHHHHHHHHHGHHHFHHHHHFHHHHHFHHHHHHHHHHFHHHGFHHFGHHHHHHHHHEFHHHHHGHHGGHHGHHHHEGH=CHG@E