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Initial creation of CRAM validation / test files
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The files are numbered such that a natural sort order will mean the
earlier files may be decodable without yet being able to decode any of
the later files.  Therefore this may optionally be considered as a
roadmap for development of new CRAM decoders.

Indices are also tested.
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@jkbonfield
jkbonfield committed Jun 29, 2020
1 parent 9f2b437 commit 4e60e79
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586 changes: 586 additions & 0 deletions test/cram/3.0/CRAM.md
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0100_header1.sam
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@HD VN:1.6
@SQ SN:chr1 LN:1000 M5:258e88dcbd3cd44d8e7ab43f6ecb6af0
@CO SAM header
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0101_header2.sam
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@HD VN:1.6
@SQ SN:chr1 LN:1000 M5:258e88dcbd3cd44d8e7ab43f6ecb6af0
@CO SAM header
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0200_cmpr_hdr.sam
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@HD VN:1.6
@SQ SN:chr1 LN:1000 M5:258e88dcbd3cd44d8e7ab43f6ecb6af0
@CO SAM header
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4 changes: 4 additions & 0 deletions test/cram/3.0/passed/0300_unmapped.sam
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@HD VN:1.6
@SQ SN:chr1 LN:1000 M5:258e88dcbd3cd44d8e7ab43f6ecb6af0
@CO SAM header
x 4 * 0 0 * * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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5 changes: 5 additions & 0 deletions test/cram/3.0/passed/0301_unmapped.sam
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@HD VN:1.6
@SQ SN:chr1 LN:1000 M5:258e88dcbd3cd44d8e7ab43f6ecb6af0
@CO SAM header
x 4 * 0 0 * * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
y 4 * 0 0 * * 0 0 NNTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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6 changes: 6 additions & 0 deletions test/cram/3.0/passed/0302_unmapped.sam
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@HD VN:1.6
@SQ SN:chr1 LN:1000 M5:258e88dcbd3cd44d8e7ab43f6ecb6af0
@CO SAM header
x 4 * 0 0 * * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
y 77 * 0 0 * * 0 0 NNTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
y 141 * 0 0 * * 0 0 TAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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6 changes: 6 additions & 0 deletions test/cram/3.0/passed/0303_unmapped.sam
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@HD VN:1.6
@SQ SN:chr1 LN:1000 M5:258e88dcbd3cd44d8e7ab43f6ecb6af0
@CO SAM header
x 4 * 0 0 * * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
y 77 * 0 0 * * 0 0 NNTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
y 141 * 0 0 * * 0 0 TAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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2 changes: 2 additions & 0 deletions test/cram/3.0/passed/0400_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd
fwdmatch 0 CHROMOSOME_I 1000 40 100M * 0 0 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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4 changes: 4 additions & 0 deletions test/cram/3.0/passed/0401_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd
@PG ID:samtools PN:samtools VN:1.10-74-gd7757f2 CL:samtools fixmate -O sam _.sam -
match 99 CHROMOSOME_I 1000 40 100M * 0 0 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M * 0 0 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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4 changes: 4 additions & 0 deletions test/cram/3.0/passed/0402_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd
@PG ID:samtools PN:samtools VN:1.10-74-gd7757f2 CL:samtools fixmate -O sam _.sam -
match 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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4 changes: 4 additions & 0 deletions test/cram/3.0/passed/0403_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd
@PG ID:samtools PN:samtools VN:1.10-74-gd7757f2 CL:samtools fixmate -O sam _.sam -
match 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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4 changes: 4 additions & 0 deletions test/cram/3.0/passed/0500_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
@PG ID:samtools PN:samtools VN:1.10-74-gd7757f2 CL:samtools fixmate -O sam _.sam -
match 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0501_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
match 99 CHROMOSOME_I 1000 40 100M = 1200 300 CTTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 GGGTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAAGGG #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0502_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
match 99 CHROMOSOME_I 1000 40 100M = 1200 300 RTTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATR #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 YYGTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAAGYY #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0503_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
match 99 CHROMOSOME_I 1000 40 100M = 1200 300 RTTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATR #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 YYGTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAAGYY #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0504_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
match 99 CHROMOSOME_I 1001 40 10H1S89M10S1H = 1200 290 RTTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATR #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 3H91M9S5H = 1001 -290 YYGTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAAGYY #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0505_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
match 99 CHROMOSOME_I 1000 40 20M5D2M1D42M5I1M1I29M = 1200 300 ATTTTTCGGGTTTTTTGAAAATGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTGAAAGTATCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0506_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
match 99 CHROMOSOME_I 1000 40 20M5D2M1D42M1P3I1P1M1I29M = 1200 300 ATTTTTCGGGTTTTTTGAAAATGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTAAATATCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0507_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
match 99 CHROMOSOME_I 1000 40 20M5D2M1D10M21N11M1P3I1P1M1I29M = 1200 300 ATTTTTCGGGTTTTTTGAAAATGTAGCTACAGAAAGTTTGTTTAAATATCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Binary file added test/cram/3.0/passed/0600_mapped.cram
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0600_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
match 99 CHROMOSOME_I 1000 40 20M5D2M1D10M21N11M1P3I1P1M1I29M = 1200 300 ATTTTTCGGGTTTTTTGAAAATGTAGCTACAGAAAGTTTGTTTAAATATCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 CCCTTTCAGAAAAATTATTTTTAAGAATTTTTCATRYTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCTAAAGGG #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0601_mapped.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
match 99 CHROMOSOME_I 1000 40 20M5D2M1D10M21N11M1P3I1P1M1I29M = 1200 300 ATTTTTCGGGTTTTTTGAAAATGTAGCTACAGAAAGTTTGTTTAAATATCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
match 147 CHROMOSOME_I 1200 40 100M = 1000 -300 CCCTTTCAGAAAAATTATTTTTAAGAATTTTTCATRYTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCTAAAGGG #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0700_tag.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC II:i:3
r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC II:i:3
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0701_tag.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC II:i:3
r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
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5 changes: 5 additions & 0 deletions test/cram/3.0/passed/0702_tag.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CV:i:299792458 PI:f:3.14159
r2 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CV:i:299792458 PI:f:3.14159
r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Z0:Z:299792458 Ohms Me:Z:9.1093837015x10^-31 kg
r2 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Z0:Z:299792458 Ohms Me:Z:9.1093837015x10^-31 kg Mp:Z:1.67262192370x10^-27 kg
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0703_tag.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC I0:i:0 I1:i:1 I2:i:127 I3:i:128 I4:i:255 I5:i:256 I6:i:32767 I7:i:32768 I8:i:65535 I9:i:65536 IA:i:2147483647 IB:i:4294967295
r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC i1:i:-1 i2:i:-127 i3:i:-128 i4:i:-255 i5:i:-256 i6:i:-32767 i7:i:-32768 i8:i:-65535 i9:i:-65536 iA:i:-2147483647 iB:i:-2147483648
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0704_tag.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC a0:A:!
r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC a0:A:~
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0705_tag.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC H0:H:0000BAD0FF1CE4C0FFEE0000
r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC H0:H: ZZ:Z:empty H1:H:
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0706_tag.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCACTCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC BF:B:f,-3e+30,-2e+20,-1e+10,0,1e+10,2e+20,3e+30 Bf:B:f,-3e-30,-2e-20,-1e-10,0,1e-10,2e-20,3e-30
r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTATTTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC BC:B:C,0,127,128,255 Bc:B:c,-128,-127,0,127 BS:B:S,0,32767,32768,65535 Bs:B:s,-32768,-32767,0,32767 BI:B:I,0,2147483647,2147483648,4294967295 Bi:B:i,-2147483648,-2147483647,0,2147483647
Binary file added test/cram/3.0/passed/0707_tag.cram
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0707_tag.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCGNGCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC MD:Z:50A0C0T47 NM:i:3
r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTCNCTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC MD:Z:50A0T0T47 NM:i:3
Binary file added test/cram/3.0/passed/0708_tag.cram
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3 changes: 3 additions & 0 deletions test/cram/3.0/passed/0708_tag.sam
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@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCGNGCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC MD:Z:50A0C48 NM:i:2
r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTCNCTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC MD:Z:50A0T48 NM:i:2
Binary file added test/cram/3.0/passed/0709_tag.cram
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7 changes: 7 additions & 0 deletions test/cram/3.0/passed/0709_tag.sam
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@@ -0,0 +1,7 @@
@SQ SN:CHROMOSOME_I LN:1009800 M5:8ede36131e0dbf3417807e48f77f3ebd UR:/nfs/users/nfs_j/jkb/work/samtools_master/hts-specs/test/CRAM/passed/ce.fa
@RG ID:rg SM:test
@RG ID:rg2 SM:test
r1 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCGNGCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg
r1 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTCNCTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg
r2 99 CHROMOSOME_I 1000 40 100M = 1200 300 ATTTTTCGGGTTTTTTGAAATGAATATCGTAGCTACAGAAACGGTTGTGCGNGCATCTGAAAGTTTGTTTTTCTTGTTTTCTTGCACTTTGTGCAGAATT #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg2
r2 147 CHROMOSOME_I 1200 40 100M = 1000 -300 TTTTTTTAGAAAAATTATTTTTAAGAATTTTTCATTTTAGGAATATTGTTCNCTCAGAAAATAGCTAAATGTGATTTCTGTAATTTTGCCTGCCAAATTC #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:rg2
Binary file added test/cram/3.0/passed/0710_tag.cram
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