| Previous changeset 0:5dcbce4f5971 (2012-03-30) Next changeset 2:9710e9bcc5f3 (2014-03-11) |
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Commit message:
Add tool_dependencies.xml and test-data |
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modified:
samtools_filter.xml |
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added:
README test-data/bam_to_sam_in1.sam test-data/bam_to_sam_in2.sam tool_dependencies.xml |
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| diff -r 5dcbce4f5971 -r f2e4e81f3639 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Apr 01 10:57:16 2013 -0500 |
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| @@ -0,0 +1,29 @@ +**What it does** + +This tool uses the samtools view command in SAMTools toolkit to filter a SAM or BAM file on the MAPQ (mapping quality), FLAG bits, Read Group, Library, or region. + +**Input** + +Input is either a SAM or BAM file. + +**Output** + +The output file will be of the same format a the Input file, filtered by the selected options. + +**Options** + +Filtering by read group or library requires headers in the input SAM or BAM file. + +If regions are specified, only alignments overlapping the specified regions will be output. An alignment may be given multiple times if it is overlapping several regions. +A region can be presented, for example, in the following format + + chr2 (the whole chr2) + chr2:1000000 (region starting from 1,000,000bp) + chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points). + +Note: The coordinate is 1-based. + +Multiple regions may be specified, separated by a space character + + chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX + |
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| diff -r 5dcbce4f5971 -r f2e4e81f3639 samtools_filter.xml --- a/samtools_filter.xml Fri Mar 30 16:36:54 2012 -0400 +++ b/samtools_filter.xml Mon Apr 01 10:57:16 2013 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="samtools_filter" name="Filter SAM or BAM" version="1.1.0"> +<tool id="samtools_filter" name="Filter SAM or BAM" version="1.1.1"> <description>files on FLAG MAPQ RG LN or by region</description> <requirements> - <requirement type="package">samtools</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> </requirements> <!-- samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] <in.bam>|<in.sam> [region1 [...]] |
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| diff -r 5dcbce4f5971 -r f2e4e81f3639 test-data/bam_to_sam_in1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam_to_sam_in1.sam Mon Apr 01 10:57:16 2013 -0500 |
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| @@ -0,0 +1,14 @@ +@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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| diff -r 5dcbce4f5971 -r f2e4e81f3639 test-data/bam_to_sam_in2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam_to_sam_in2.sam Mon Apr 01 10:57:16 2013 -0500 |
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| @@ -0,0 +1,25 @@ +@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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| diff -r 5dcbce4f5971 -r f2e4e81f3639 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Apr 01 10:57:16 2013 -0500 |
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| @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.18"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="samtools_0_1_18" owner="devteam" changeset_revision="a7936f4ea405" /> + </package> +</tool_dependency> + |