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Update samtools to 1.4 and migrate to iuc. #1240

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Update samtools to 1.4 and migrate to iuc. #1240

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14 changes: 14 additions & 0 deletions suites/suite_samtools_1_4/.shed.yml
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categories:
- SAM
description: A suite of Galaxy utilities associated with version 1.4 of the SAMtools package.
long_description: |
SAM (Sequence Alignment/Map) format is a generic format for storing
large nucleotide sequence alignments. This repository suite associates selected
repositories containing Galaxy utilities that require version 1.4 of the SAMTools
package. These associated Galaxy utilities consist of a Galaxy Data Manager contained
in the repository named data_manager_sam_fasta_index_builder and Galaxy tools contained
in several separate repositories.
name: suite_samtools_1_4
owner: iuc
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/suites/suite_samtools_1_4
type: repository_suite_definition
19 changes: 19 additions & 0 deletions suites/suite_samtools_1_4/repository_dependencies.xml
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<?xml version="1.0"?>
<repositories description="A suite of Galaxy tools designed to work with version 1.4 of the SAMtools package.">
<repository name="data_manager_sam_fasta_index_builder" owner="iuc" />
<repository name="bam_to_sam" owner="iuc" />
<repository name="sam_to_bam" owner="iuc" />
<repository name="samtools_bam_to_cram" owner="iuc" />
<repository name="samtools_cram_to_bam" owner="iuc" />
<repository name="samtools_bedcov" owner="iuc" />
<repository name="samtools_calmd" owner="iuc" />
<repository name="samtools_flagstat" owner="iuc" />
<repository name="samtools_idxstats" owner="iuc" />
<repository name="samtools_mpileup" owner="iuc" />
<repository name="samtools_reheader" owner="iuc" />
<repository name="samtools_rmdup" owner="iuc" />
<repository name="samtools_slice_bam" owner="iuc" />
<repository name="samtools_sort" owner="iuc" />
<repository name="samtools_split" owner="iuc" />
<repository name="samtools_stats" owner="iuc" />
</repositories>
13 changes: 13 additions & 0 deletions tool_collections/samtools/bam_to_cram/.shed.yml
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categories:
- Convert Formats
- SAM
description: Converts alignments in BAM format to CRAM format.
long_description: |
This tool uses the SAMtools toolkit to convert BAM to CRAM files. The CRAM
format does additional compression relative to the reference genome which
makes the compression more effictient in terms of file size.
name: samtools_bam_to_cram
owner: iuc
homepage_url: https://samtools.github.io/
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram
type: unrestricted
1 change: 1 addition & 0 deletions tool_collections/samtools/bam_to_cram/macros.xml
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../macros.xml
123 changes: 123 additions & 0 deletions tool_collections/samtools/bam_to_cram/samtools_bam_to_cram.xml
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<tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@[email protected]">
<description>convert BAM alignments to CRAM format</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<expand macro="version_command" />
<expand macro="stdio" />
<command>
<![CDATA[
#if str( $input_alignment.metadata.bam_index ) != "None":
ln
-f
-s
"${input_alignment.metadata.bam_index}"
"${input_alignment}.bai"
&&
#end if

samtools view
#if $parameter_regions.target_region == "regions_bed_file"
-L "${parameter_regions.regions_bed_file}"
#end if

-@\${GALAXY_SLOTS:-2}
-C
-T "${reference_source.input_reference}"
-o "$output_alignment"
"$input_alignment"

#if $parameter_regions.target_region == "region"
"${parameter_regions.region_string}"
#end if
]]>
</command>

<inputs>
<param name="input_alignment" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/>
<conditional name="reference_source">
<param name="reference_source_selector" type="select" label="Load reference genome from">
<option value="cached">Local cache</option>
<option value="history">History</option>
</param>
<when value="cached">
<param name="input_reference" type="select" format="fasta" label="Genome reference FASTA file">
<options from_data_table="all_fasta">
<filter type="data_meta" ref="input_alignment" key="dbkey" column="1" />
</options>
<validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
</param>
</when>
<when value="history">
<param name="input_reference" type="data" format="fasta" label="Genome reference FASTA file"/>
</when>
</conditional>
<conditional name="parameter_regions">
<param name="target_region" type="select" label="Choose conversion within specific genomic region(s)">
<option value="entire_input_file">Entire BAM alignment file</option>
<option value="region">Specific region</option>
<option value="regions_bed_file">List of specific regions (BED file)</option>
</param>
<when value="entire_input_file" />
<when value="region">
<param name="region_string" type="text" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:start-end" />
</when>
<when value="regions_bed_file">
<param name="regions_bed_file" type="data" format="bed" label="only include reads overlapping this BED FILE" help="-L"/>
</when>
</conditional>
</inputs>

<outputs>
<data format="cram" name="output_alignment" label="$tool.name on ${on_string}.cram"></data>
</outputs>

<tests>
<test>
<param name="input_alignment" value="test.bam" ftype="bam" />
<param name="reference_source_selector" value="history" />
<param name="input_reference" value="test.fa" />
<param name="target_region" value="entire_input_file" />

<output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
</test>
<test>
<param name="input_alignment" value="test.sam" ftype="sam" />
<param name="reference_source_selector" value="history" />
<param name="input_reference" value="test.fa" />
<param name="target_region" value="entire_input_file" />

<output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
</test>
<test>
<param name="input_alignment" value="test.bam" ftype="bam" />
<param name="reference_source_selector" value="history" />
<param name="input_reference" value="test.fa" />
<param name="target_region" value="region" />
<param name="region_string" value="CHROMOSOME_I" />

<output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
</test>
<test>
<param name="input_alignment" value="test.bam" ftype="bam" />
<param name="reference_source_selector" value="history" />
<param name="input_reference" value="test.fa" />
<param name="target_region" value="regions_bed_file" />
<param name="regions_bed_file" value="test.bed" ftype="bed" />

<output name="output_alignment" file="test.cram" compare="sim_size" delta="250" />
</test>
</tests>

<help>

**What this tool does**

Converts alignments from the BAM format to the CRAM format using the SAMTools_ toolkit. The CRAM format does additional compression relative to the reference genome which makes the compression in terms of file size more effictient.

.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
</help>

<expand macro="citations"></expand>
</tool>
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1 change: 1 addition & 0 deletions tool_collections/samtools/bam_to_cram/test-data/test.bed
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CHROMOSOME_I 1 120
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3 changes: 3 additions & 0 deletions tool_collections/samtools/bam_to_cram/test-data/test.fa
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>CHROMOSOME_I
gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc
ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct
1 change: 1 addition & 0 deletions tool_collections/samtools/bam_to_cram/test-data/test.fa.fai
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CHROMOSOME_I 100 14 50 51
15 changes: 15 additions & 0 deletions tool_collections/samtools/bam_to_cram/test-data/test.sam
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@HD VN:1.4 SO:unsorted
@SQ SN:CHROMOSOME_I LN:100
@RG ID:UNKNOWN SM:UNKNOWN
@PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5
@PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2
SRR065390.14978392 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:1 XM:i:5 XN:i:0 XO:i:1 AS:i:-18 XS:i:-18 YT:Z:UU
SRR065390.921023 16 CHROMOSOME_I 3 12 100M * 0 0 CTAAGCCTAAATCTAAGCCTAACCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################################???88:;98768700000<>:BBA?BBAB?BBBBBBBB>B>BB::;?:00000 RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-13 YT:Z:UU
SRR065390.1871511 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA <?@<@A8>0:BB@>B<=B@???@=8@B>BB@CA@DACDCBBCCCA@CCCCACCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
SRR065390.3743423 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ##################?6@:7<=@3=@ABAAB>BDBBABADABDDDBDDBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
SRR065390.4251890 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###########@BB=BCBBC?B>B;>B@@ADBBB@DBBBBDCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
SRR065390.5238868 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA @,=@@D8D;?BBB>;?BBB==BB@D;>D>BBB>BBDDB<DABADCACDCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
SRR065390.6023338 0 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAAGCTAC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCDDDBCCABB=DABBA?################ RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-6 YT:Z:UU
SRR065390.6815812 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############?@.@?B;B0B=;<DADB@@BDDBBDDBCBCBD@CCDCCCCCCCDCCCCCCCCACCCCCCCCCCBCCCCCCDCCCCCCCCCCCBCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
SRR065390.6905811 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #######################BB@>A<BC>@@BCCB@=BACBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
SRR065390.8289592 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################A?@C9@@BC=AABDD@A@DC@CB=@BA?6@CCAAC@+CCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
11 changes: 11 additions & 0 deletions tool_collections/samtools/bam_to_sam/.shed.yml
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categories:
- SAM
- Convert Formats
description: Converts BAM format to SAM format.
long_description: |
This tool uses the SAMtools toolkit to produce a SAM file from a BAM file.
name: bam_to_sam
owner: iuc
homepage_url: http://www.htslib.org/
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam
type: unrestricted
54 changes: 54 additions & 0 deletions tool_collections/samtools/bam_to_sam/bam_to_sam.xml
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<tool id="bam_to_sam" name="BAM-to-SAM" version="2.1">
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<expand macro="version_command" />
<expand macro="stdio" />
<description>convert BAM to SAM</description>
<command>
<![CDATA[
samtools view -o "${output1}" ${header} "${input1}"
]]>
</command>
<inputs>
<param format="bam" label="BAM File to Convert" name="input1" type="data" />
<param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
<option value="-h">Include header in SAM output (-h)</option>
<option value="-H">Print header only (-H)</option>
<option value="">Exclude header</option>
</param>
</inputs>
<outputs>
<data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
</outputs>
<tests>
<test>
<param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
<param name="header" value="-h" />
<output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
</test>
<test>
<param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
<param name="header" value="-H" />
<output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
</test>
<test>
<param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
<param name="header" value="" />
<output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
</test>
</tests>
<help>
<![CDATA[

**What it does**

Converts BAM dataset to SAM using ``samtools view`` command::

samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM]

]]>
</help>
<expand macro="citations"></expand>
</tool>
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../macros.xml
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@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
@RG ID:0 SM:Hi,Mom!
@PG ID:1 PN:Hey! VN:2.0
both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
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@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:10001
@SQ SN:chr2 LN:100001
@SQ SN:chr3 LN:10001
@SQ SN:chr4 LN:1001
@RG ID:rg1 SM:s1
@RG ID:rg2 SM:s3
bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2
bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2
bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2
bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2
bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2
bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2
bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2
bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1
bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1
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@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
@RG ID:0 SM:Hi,Mom!
@PG ID:1 PN:Hey! VN:2.0
both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0
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