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Add 4 CRAM compliance tests from htslib #1185

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merged 5 commits into from
Oct 5, 2018
Merged

Add 4 CRAM compliance tests from htslib #1185

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1ebe395
add 4 compliance tests from htslib
jmthibault79 Oct 4, 2018
942da36
samtools versions
jmthibault79 Oct 4, 2018
3306335
add c2#pad and md#1, and link others to issues
jmthibault79 Oct 5, 2018
c47f7d1
actually add the files
jmthibault79 Oct 5, 2018
cac1ba3
Add c2.fa.fai and md.fa.fai
jmthibault79 Oct 5, 2018
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8 changes: 6 additions & 2 deletions src/test/java/htsjdk/samtools/CRAMComplianceTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -41,14 +41,18 @@ public Object[][] getPartialVerificationData() {
{"c1#noseq"}, // unsigned attributes: https://github.com/samtools/htsjdk/issues/499
{"c1#unknown"}, // unsigned attributes: https://github.com/samtools/htsjdk/issues/499
{"ce#5b"}, // reads with no read bases: https://github.com/samtools/htsjdk/issues/509
{"ce#1000"}, // copied from htslib - need to investigate record mismatch
{"ce#tag_depadded"},// reads with no read bases: https://github.com/samtools/htsjdk/issues/509
{"ce#tag_padded"}, // reads with no read bases: https://github.com/samtools/htsjdk/issues/509
{"ce#unmap"}, // unmapped reads with non-zero MAPQ value that is not restored
// https://github.com/samtools/htsjdk/issues/714
{"xx#triplet"}, // the version 2.1 variant of this file has a bad insertSize, which is
// probably residual detritus from https://github.com/samtools/htsjdk/issues/364
{"xx#minimal"}, // cigar string "5H0M5H" is restored as "10H"
// https://github.com/samtools/htsjdk/issues/713
{"xx#repeated"}, // copied from htslib - need to investigate record mismatch
{"xx#tlen"}, // copied from htslib - need to investigate record mismatch
{"xx#tlen2"}, // copied from htslib - need to investigate record mismatch
{"xx#triplet"}, // the version 2.1 variant of this file has a bad insertSize, which is
// probably residual detritus from https://github.com/samtools/htsjdk/issues/364
};
}

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Binary file added src/test/resources/htsjdk/samtools/cram/ce#1000.2.1.cram
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Binary file added src/test/resources/htsjdk/samtools/cram/ce#1000.3.0.cram
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1,005 changes: 1,005 additions & 0 deletions src/test/resources/htsjdk/samtools/cram/ce#1000.sam
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Binary file added src/test/resources/htsjdk/samtools/cram/xx#repeated.2.1.cram
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Binary file added src/test/resources/htsjdk/samtools/cram/xx#repeated.3.0.cram
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7 changes: 7 additions & 0 deletions src/test/resources/htsjdk/samtools/cram/xx#repeated.sam
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@@ -0,0 +1,7 @@
@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 **********
Binary file modified src/test/resources/htsjdk/samtools/cram/xx#tlen.2.1.cram
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Binary file modified src/test/resources/htsjdk/samtools/cram/xx#tlen.3.0.cram
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34 changes: 34 additions & 0 deletions src/test/resources/htsjdk/samtools/cram/xx#tlen.sam
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@@ -0,0 +1,34 @@
@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 *****
Binary file modified src/test/resources/htsjdk/samtools/cram/xx#tlen2.2.1.cram
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Binary file modified src/test/resources/htsjdk/samtools/cram/xx#tlen2.3.0.cram
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36 changes: 36 additions & 0 deletions src/test/resources/htsjdk/samtools/cram/xx#tlen2.sam
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@@ -0,0 +1,36 @@
@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 *****