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Add 6 CRAM compliance tests from htslib (#1185)
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@SQ SN:c2 LN:9 | ||
@CO | ||
@CO mpileup example from https://github.com/samtools/htslib/issues/59 | ||
@CO with additional Pad cigar operations | ||
@CO | ||
@CO c2 CC***AA**T**AA***CC | ||
@CO | ||
@CO +s1 CT***AA**T**AA***TC | ||
@CO +s1b CT*******T*******TC | ||
@CO +s2 CT*****G***G*****TC | ||
@CO +s2p CT*****G***G*****TC | ||
@CO +s3 CT*****GG*GG*****TC | ||
@CO +s3b CT****CGGCGGC****TC | ||
@CO +s4 CT***AAG***GAA***TC | ||
@CO +s4p CT***AAG***GAA***TC | ||
@CO +s5 CTGGG*********GGGTC | ||
@CO | ||
s1 0 c2 1 0 9M * 0 0 CTAATAATC XXXXXXXXX | ||
s1b 0 c2 1 0 2M2D1M2D2M * 0 0 CTTTC * | ||
s2 0 c2 1 0 2M2D1I1D1I2D2M * 0 0 CTGGTC * | ||
s2p 0 c2 1 0 2M2D1I1P1D1P1I2D2M * 0 0 CTGGTC * | ||
s3 0 c2 1 0 2M2D2I1D2I2D2M * 0 0 CTGGGGTC * | ||
s3b 0 c2 1 0 2M1D1M2I1M2I1M1D2M * 0 0 CTCGGCGGCTC * | ||
s4 0 c2 1 0 4M1I1D1I4M * 0 0 CTAAGGAATC * | ||
s4p 0 c2 1 0 4M1I1P1D1P1I4M * 0 0 CTAAGGAATC * | ||
s5 0 c2 1 0 2M3I5D3I2M * 0 0 CTGGGGGGTC * |
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>c2 | ||
CCAATAACC |
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c2 9 4 9 10 |
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src/test/resources/htsjdk/samtools/cram/ce#1000.sam
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@HD VN:1.0 SO:coordinate | ||
@SQ SN:a LN:40 | ||
x 0 a 1 255 40M * 0 0 AAAAAAAAAACCCCCCCCYNNRGGGGGGGGTTTTTTTTTT * NM:i:2 MD:Z:19N0N19 | ||
x* 0 a 1 255 40M * 0 0 CAAAAAAAANNCCCCCCCYNNRGGGGGGGGTTTTTTTTTC * NM:i:6 MD:Z:0A8A0C8N0N18T0 | ||
xIP 0 a 1 255 1I10M1I10M2I10M2P3I2P10M1I * 0 0 NAAAAAAAAAAGCCCCCCCCCCAAGGGGGGGGGGCCCTTTTTTTTTTN * NM:i:12 MD:Z:18Y0N0N0R18 | ||
xIP* 0 a 1 255 1I10M1I10M2I10M2P3I2P10M1I * 0 0 NCAAAAAAAAAGCCCCCCCCCCAAGGGGGGGGGACCCATTTTTTTTCN * NM:i:16 MD:Z:0A17Y0N0N0R7G0T8T0 | ||
xD 0 a 1 255 9M1D8M2D7M3D6M * 0 0 AAAAAAAAACCCCCCYNNRGGGGGTTTTTT * NM:i:9 MD:Z:9^A6C0C0^YN0N6^GGG6 | ||
xD* 0 a 1 255 9M1D8M2D7M3D6M * 0 0 CAAAAAAANNCCCCCCTTGGGGGGTTTTTA * NM:i:13 MD:Z:0A7A0^A0C6C0^YN0N0R5^GGG5T0 | ||
xN 0 a 1 255 10M20N10M * 0 0 AAAAAAAAAATTTTTTTTTT * NM:i:0 MD:Z:20 | ||
xN* 0 a 1 255 10M20N10M * 0 0 CAAAAAAACCAATTTTTTTA * NM:i:6 MD:Z:0A7A0A0T0T7T0 | ||
xS 0 a 11 255 5H10S20M10S5H * 0 0 AAAAAAAAAACCCCCCCCYNNRGGGGGGGGTTTTTTTTTT * NM:i:2 MD:Z:9N0N9 | ||
xS* 0 a 11 255 5H10S20M10S5H * 0 0 CAAAATAAAACCCCCCCCYNNRGGGGGGGGTTTTATTTTC * NM:i:2 MD:Z:9N0N9 |
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>a | ||
AAAAAAAAAACCCCCCCCYNNRGGGGGGGGTTTTTTTTTT | ||
|
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a 40 3 40 41 |
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@SQ SN:xx LN:20 | ||
S 67 xx 1 1 10M = 11 20 AAAAAAAAAA ********** | ||
S 131 xx 11 1 10M = 1 -20 TTTTTTTTTT ********** | ||
S 67 xx 1 1 10M = 11 20 AAAAAAAAAA ********** | ||
S 131 xx 11 1 10M = 1 -20 TTTTTTTTTT ********** | ||
S 67 xx 1 1 10M = 11 20 AAAAAAAAAA ********** | ||
S 131 xx 11 1 10M = 1 -20 TTTTTTTTTT ********** |
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@CO xx has been encoded using the SAM spec; leftmost to rightmost | ||
@CO yy has been encoded using bwa/picard methods; 5' to 3' | ||
@CO | ||
@CO 00000000011111111112 | ||
@CO 12345678901234567890 | ||
@CO AAAAAAAAAATTTTTTTTTT | ||
@CO 1>>>> <<<<2 x1 | ||
@CO | ||
@CO 1>>>> x2 | ||
@CO <<<<2 | ||
@CO | ||
@CO 1>>>> x3 (7..15 vs 10..11) | ||
@CO <<<<2 | ||
@CO | ||
@CO <<<<2 1>>>> x4 (1..20 vs 16..5) | ||
@CO | ||
@SQ SN:xx LN:20 | ||
@SQ SN:yy LN:20 | ||
x1 99 xx 1 1 5M = 16 20 AAAAA ***** | ||
x1 147 xx 16 1 5M = 1 -20 TTTTT ***** | ||
x2 99 xx 7 1 5M = 10 8 AAAAT ***** | ||
x2 147 xx 10 1 5M = 7 -8 ATTTT ***** | ||
x3 147 xx 7 1 5M = 10 8 AAAAT ***** | ||
x3 99 xx 10 1 5M = 7 -8 ATTTT ***** | ||
x4 147 xx 1 1 5M = 16 20 AAAAA ***** | ||
x4 99 xx 16 1 5M = 1 -20 TTTTT ***** | ||
y1 99 yy 1 1 5M = 16 20 AAAAA ***** | ||
y1 147 yy 16 1 5M = 1 -20 TTTTT ***** | ||
y2 99 yy 7 1 5M = 10 8 AAAAT ***** | ||
y2 147 yy 10 1 5M = 7 -8 ATTTT ***** | ||
y3 147 yy 7 1 5M = 10 -2 AAAAT ***** | ||
y3 99 yy 10 1 5M = 7 2 ATTTT ***** | ||
y4 147 yy 1 1 5M = 16 10 AAAAA ***** | ||
y4 99 yy 16 1 5M = 1 -10 TTTTT ***** |
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src/test/resources/htsjdk/samtools/cram/xx#tlen2.2.1.cram
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src/test/resources/htsjdk/samtools/cram/xx#tlen2.3.0.cram
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@CO As per xx#tlen.sam but every read is unsorted with partner | ||
@CO | ||
@CO xx has been encoded using the SAM spec; leftmost to rightmost | ||
@CO yy has been encoded using bwa/picard methods; 5' to 3' | ||
@CO | ||
@CO 00000000011111111112 | ||
@CO 12345678901234567890 | ||
@CO AAAAAAAAAATTTTTTTTTT | ||
@CO 1>>>> <<<<2 x1 | ||
@CO | ||
@CO 1>>>> x2 | ||
@CO <<<<2 | ||
@CO | ||
@CO 1>>>> x3 (7..15 vs 10..11) | ||
@CO <<<<2 | ||
@CO | ||
@CO <<<<2 1>>>> x4 (1..20 vs 16..5) | ||
@CO | ||
@SQ SN:xx LN:20 | ||
@SQ SN:yy LN:20 | ||
x1 147 xx 16 1 5M = 1 -20 TTTTT ***** | ||
x1 99 xx 1 1 5M = 16 20 AAAAA ***** | ||
x2 147 xx 10 1 5M = 7 -8 ATTTT ***** | ||
x2 99 xx 7 1 5M = 10 8 AAAAT ***** | ||
x3 99 xx 10 1 5M = 7 -8 ATTTT ***** | ||
x3 147 xx 7 1 5M = 10 8 AAAAT ***** | ||
x4 99 xx 16 1 5M = 1 -20 TTTTT ***** | ||
x4 147 xx 1 1 5M = 16 20 AAAAA ***** | ||
y1 147 yy 16 1 5M = 1 -20 TTTTT ***** | ||
y1 99 yy 1 1 5M = 16 20 AAAAA ***** | ||
y2 147 yy 10 1 5M = 7 -8 ATTTT ***** | ||
y2 99 yy 7 1 5M = 10 8 AAAAT ***** | ||
y3 99 yy 10 1 5M = 7 2 ATTTT ***** | ||
y3 147 yy 7 1 5M = 10 -2 AAAAT ***** | ||
y4 99 yy 16 1 5M = 1 -10 TTTTT ***** | ||
y4 147 yy 1 1 5M = 16 10 AAAAA ***** |