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readding the files i deleted by mistake
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emeryj committed Jan 3, 2019
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243 changes: 243 additions & 0 deletions ...g/broadinstitute/hellbender/tools/spark/RevertSamSpark/revertsamspark/missing-rg-info.sam
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3 changes: 3 additions & 0 deletions ...hellbender/tools/spark/RevertSamSpark/revertsamspark/revert_sam_bad_header_output_map.txt
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FOO OUTPUT
rg1 my_rg_1.ubam
rg2 my_rg_2.ubam
22 changes: 22 additions & 0 deletions .../broadinstitute/hellbender/tools/spark/RevertSamSpark/revertsamspark/revert_sam_basic.sam
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@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:101
@SQ SN:chr2 LN:101
@SQ SN:chr3 LN:101
@SQ SN:chr4 LN:101
@SQ SN:chr5 LN:101
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
@RG ID:0 SM:Hi,Mom! LB:my-library PL:ILLUMINA
@RG ID:1 SM:Hi,Mom! LB:my-library PL:ILLUMINA
@RG ID:2 SM:Hi,Mom! LB:my-library PL:ILLUMINA
@RG ID:3 SM:Hi,Mom! LB:my-library PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
both_reads_align_clip_marked 1107 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 PG:Z:1 NM:i:0 MQ:i:255 XT:Z:foo OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
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:1 PG:Z:1 NM:i:3 MQ:i:255 XT:Z:foo OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:2 PG:Z:1 NM:i:8 MQ:i:255 XT:Z:foo2 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1 PG:Z:1 NM:i:1 MQ:i:255 XT:Z:foo2 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1 PG:Z:1 NM:i:1 MQ:i:255 XT:Z:foo2 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
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 PG:Z:1 NM:i:5 MQ:i:255 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
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:2 PG:Z:1 NM:i:6 MQ:i:255 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
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:1 PG:Z:1
21 changes: 21 additions & 0 deletions ...llbender/tools/spark/RevertSamSpark/revertsamspark/revert_sam_sample_library_override.sam
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@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:101
@SQ SN:chr2 LN:101
@SQ SN:chr3 LN:101
@SQ SN:chr4 LN:101
@SQ SN:chr5 LN:101
@SQ SN:chr6 LN:101
@SQ SN:chr7 LN:404
@SQ SN:chr8 LN:202
@RG ID:0 SM:Hi,Mom! LB:my-library PL:ILLUMINA
@RG ID:1 SM:Hi,Dad! LB:my-library PL:ILLUMINA
@RG ID:2 SM:Hi,Mom! LB:my-other-library PL:ILLUMINA
@PG ID:1 PN:Hey! VN:2.0
both_reads_align_clip_marked 1107 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 PG:Z:1 NM:i:0 MQ:i:255 XT:Z:foo OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
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:1 PG:Z:1 NM:i:3 MQ:i:255 XT:Z:foo OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:2 PG:Z:1 NM:i:8 MQ:i:255 XT:Z:foo2 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1 PG:Z:1 NM:i:1 MQ:i:255 XT:Z:foo2 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:1 PG:Z:1 NM:i:1 MQ:i:255 XT:Z:foo2 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
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 PG:Z:1 NM:i:5 MQ:i:255 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
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:2 PG:Z:1 NM:i:6 MQ:i:255 OQ:Z:11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
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:1 PG:Z:1
5 changes: 5 additions & 0 deletions ...dinstitute/hellbender/tools/spark/RevertSamSpark/revertsamspark/revert_sam_single_end.sam
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@HD VN:1.5 SO:queryname
@RG ID:A SM:foo LB:foo PL:illumina PU:Illumina CN:Broad
read1 4 * 0 0 * * 0 0 AAACCTACTTTGTTGAGAGTTTTTATTAACAGATGTTCAATTATATAAAAAAACTGAGTATTAATATATCCTCGTTCTTACTTTTATAGGACATTAATATGCAGCGGGGGGGGGGACTGCTCAAT CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGF RG:Z:A
read2 4 * 0 0 * * 0 0 AGCGGGGGCTGGCCCAGGCCCTATGGGCACTCACACCCCCTTCCTACCACGCCCCGGGCGCCCTCAGCCCCTGCCGTGGCCGTGGGGGGGGGGGAAGGCTCCAGGGTTCTGCAGACTTGGAACTT <<=<</EE<EBBB>BFGBGGDBE>@>D0</<11BF1/ECD/DEG>0F@0FB<F/E<<GG/:E///C//@GGEGGG6EC.89C>.6@D@=/..@8@@.8<EB.D/.C<@66//@//6:/CB/.69B RG:Z:A
read3 4 * 0 0 * * 0 0 ATGCAGCTAGTTGACAGCTGGCTTCAAGACATGCTTCCCTGTGAGGGGGGGGGGCAGGGCAGAAACCTCCCGCATCCTGCCTGACTGTAGGAGTAGCTGCTAACATCCTAATGTTAGTGGCTGGG ?BBBBGEGGGGGGGGGGGGEBFGGGGGGCGGGGEG>BFFDCGEGDGGGGEG0FGGGGBGGGGGGGGEBGGGGGGGGGGGGGGGGGGGGGEGGGGGGEGEGGGE@DGCGFGGGGGEGCF=@FGGGG RG:Z:A
3 changes: 3 additions & 0 deletions ...tute/hellbender/tools/spark/RevertSamSpark/revertsamspark/revert_sam_valid_output_map.txt
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READ_GROUP_ID OUTPUT
rg1 /path/to/my_rg_1.ubam
rg2 /path/to/my_rg_2.ubam
40 changes: 40 additions & 0 deletions ...ources/org/broadinstitute/hellbender/tools/spark/RevertSamSpark/revertsamspark/test.fasta
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>chr1
TTCATGCTGAAGCCCTCTTACGATCGTACAGATGCAAATATTAACAAACC
TTTAAGGGCAAAAAAAAAACAATACAATAATAGAGTACGTTAACACTCCA
A
>chr2
CATCTCTACAAGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATAC
TTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTTGACACCTTT
T
>chr3
CGTATGCGCTTTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAAT
AAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGGAATGTGCAA
A
>chr4
CGTGATACCAACTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATAT
TTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGGTTTGCAGCC
C
>chr5
NTCTCATTTAAAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTT
CATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCAAGACGTTATC
T
>chr6
NAATTGTTCTTAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACA
ATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACCAGTGTCGAT
C
>chr7
CAACAGAAGGGGGGATCTGTGTTTGTGTTTCGGATTTCCTGCTGAAAAGG
TTTTCGGGTCCCCCCCCCATCCCGATTTCCTTCCGCAGCTTACCTCCCGA
AACGCGGCATCCCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCA
GCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCCAGAGCATA
CAACAGAAGGGGGGATCTGTGTTTGTGTTTCGGATTTCCTGCTGAAAAGG
TTTTCGGGTCCCCCCCCCATCCCGATTTCCTTCCGCAGCTTACCTCCCGA
AACGCGGCATCCCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCA
GCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCCAGAGCATA
CAAC
>chr8
CACATCGTGAATCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGA
GAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCCTAAGATGAC
CCCAGGTTCAAATGTGCAGCCCCTTTTGAGAGATTTTTTTTTTGGGCTGG
AAAAAAGACACAGCTATTCCTAAGATGACAAGATCAGAAAAAAAGTCAAG
CA

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