/htsjdk

Update CRAM conversion and round trip tests. #720

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merged 1 commit into from Feb 8, 2017
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4 src/test/java/htsjdk/samtools/CRAMCRAIIndexerTest.java
@@ -22,7 +22,7 @@
@Test
public void testCRAIIndexerFromContainer() throws IOException {
final File CRAMFile = new File("src/test/resources/htsjdk/samtools/cram/test2.cram");
- final File refFile = new File("src/test/resources/htsjdk/samtools/cram/test2.fa");
+ final File refFile = new File("src/test/resources/htsjdk/samtools/cram/auxf.fa");
ReferenceSource refSource = new ReferenceSource(refFile);
CRAMFileReader reader = new CRAMFileReader(
CRAMFile,
@@ -55,7 +55,7 @@ public void testCRAIIndexerFromContainer() throws IOException {
@Test
public void testCRAIIndexerFromStream() throws IOException {
final File CRAMFile = new File("src/test/resources/htsjdk/samtools/cram/test2.cram");
- final File refFile = new File("src/test/resources/htsjdk/samtools/cram/test2.fa");
+ final File refFile = new File("src/test/resources/htsjdk/samtools/cram/auxf.fa");
ReferenceSource refSource = new ReferenceSource(refFile);
// get the header to use
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224 src/test/java/htsjdk/samtools/CRAMComplianceTest.java

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1 src/test/java/htsjdk/samtools/CRAMFileWriterTest.java
@@ -248,6 +248,7 @@ public void test_roundtrip_tlen_preserved() throws IOException {
SAMRecord record1 = iterator.next();
SAMRecord record2 = records.get(i++);
Assert.assertEquals(record1.getInferredInsertSize(), record2.getInferredInsertSize(), record1.getReadName());
+ Assert.assertEquals(record1, record2, record1.getReadName());
}
Assert.assertEquals(records.size(), i);
}
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BIN src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.first.8000.bam
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15 src/test/resources/htsjdk/samtools/cram/fieldarith.sam
@@ -1,15 +0,0 @@
-@SQ SN:one LN:1000
-@SQ SN:two LN:500
-@CO For each SAM record that has each listed aux field, performs these tests:
-@CO XQ is the expected result for bam_cigar2qlen()
-@CO XR is the expected result for bam_cigar2rlen()
-@CO XE is the expected result for bam_endpos()
-@CO (Note that these are all zero-based, while POS is one-based in SAM)
-r1 0 one 50 20 8M * 0 0 ATGCATGC qqqqqqqq XQ:i:8 XR:i:8 XE:i:57
-r2 0 one 100 20 50M * 0 0 ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq XQ:i:50 XR:i:50 XE:i:149
-unmapped 5 two 200 0 * two 200 0 ATGCATGC qqqqqqqq XQ:i:0 XR:i:0 XE:i:200
-hascigar 5 two 200 0 6M2S two 200 0 ATGCATGC qqqqqqqq XQ:i:8 XR:i:6 XE:i:200
-s1 0 one 300 20 2M * 0 0 AT qq XQ:i:2 XR:i:2 XE:i:301
-su1 4 * 0 0 * * 0 0 AT qq XQ:i:0 XR:i:0 XE:i:0
-su2 5 two 400 0 * two 400 0 AT qq XQ:i:0 XR:i:0 XE:i:400
-su3 4 one 500 0 2M * 0 0 AT qq XQ:i:2 XR:i:2 XE:i:500
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2 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.dict
@@ -0,0 +1,2 @@
+@HD VN:1.0 SO:unsorted
+@SQ SN:20 LN:9000 M5:46ad963a88a95089707c4639ad196126 UR:file:///Users/cmn/projects/cram/final/hum.20.fasta
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151 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.fasta
@@ -0,0 +1,151 @@
+>20
+TTGTCCCTGTATCATTTACTGAAAAGACTCTTCTTTTCCCCATTAGATGGTCTTGAAACG
+TTGTTAAAATTCAACTGACCATAGGTGTATTGGTTTATTTCTGTACTCTTAGTAGATTCC
+ATTGACCTATATCTCTATCCTTATGCCAGTACCACAGTTTTGTTTACTACAGCTTTGTAG
+TAAATTTTGAACTCTAAAGTGTTAGTTCTCTAACTTTGTTTGTTTTTCAAGAGTGTTTTG
+ACTCTTCTTACTGCATCCCTTGCATTTCCATATGGACTTTATAATCAGCCATGTCAACTT
+CTGCAAGAAAGACAGCTAGGATTTTGATAAGGATTGTGTTGAATCTGTAGTCCAATTTTG
+GGAATACTACCATGTTAACATCGTCTTCCCATCCATGCACGTGCAATAGCTTACCATTTA
+TTTGGTCTTCCTCAATTTCTGTCAACAATGATTTGTAGTTTTCAGTTGCAAGTCTTGCAC
+TTCTTTTGTTAAACTTTTTCCAAATATTTATTCTTCTTAATTACATAATTCTCATAATTA
+ATAAAATTCTGAAATTTTCTTAATTTCATTTTTGTGGCCATGCACTTTAAAACTTGCCTT
+TTAACAAGACTTCCAGATGATTCTTGTGAACATTAAGTTTGTGAAGTGCTTCTCTATTGA
+CAAACTGAACTCACGTGACATTCCACACAGCACTGGCAAATTCTGTCCCGTAACTCCGCT
+AGCTCTCCAACAAGAAGTGACTTGACGCAGCCCAAGGTTACTACTTAACACAATGAATTA
+AATGTTTTTAAATAAGAGGAAGCAATAAGATTCTAAAGGCTTTTCTGTTTTAATTTTCAT
+GCAATGGAAAACTGGTATTAAATATCTATTTAATTAGGAGGAAACTACAATGCTGACTTT
+TGTCTGAATTATGTAGATAAGTGATTCATTTGAAACAATTATTTTGATAATTGTCAATTA
+TCCATTTCATTTTAATGCATTTTTTATTCTTTTTTCAAAAATAGCAACAATTACAACAGT
+TAAACCTTATAATGAATATGTTTCCTAAACCCTGTTCTACTTTCTGGTTCCAGATCTGAC
+ACCAATTACCTTTCTGATTTTGGACAAACCACTTAATATTTGTAACTTACAATTACTTCA
+ACTGAATAATAAAAGAATTGGACTAGATTTCTCCAACATCTCTCTCTTTTGGCTTTATGT
+TAGATAATGCTAAATTTTCATCATATCCAAACATGCTATATAATTTTATGAACTGTTACA
+GAGTCAGACATAAGCAATATAAAGTATGATTCTGAATAAAGGCTGTGAAGTCTCGTTTTT
+CATACATAATTACAGGAACCGATCAAATTCAATAAAGCATTTATAGTCATGACAATATAT
+TCTCTTAACTTGCAATGTGGTTTTAGGAAACAATGAAACAAATTAAACAAATGCATGATT
+CCTTAAATTTTGTTGACTCGGGATTTAGTTACATATAAGACTCTTTTCCCCCAGCCAGAT
+TAACCCTGCTCTGTATATGTAATACGCATCTTCCCCCCAAATTTCACAATAATAATTTTA
+TGAAAATCAGTATGTAAGTTGCTGCATTGGCATGAAAGGCTACTAATGTGATATCTTTCA
+AAGATAAAGTGAACGTTTTTGTAAAAAGCCACCACACTGGAGGCATTTAACAATATTCAT
+CTTCCTATGGCATTACTACCCTAGATGTACTTTGCAATATTAATCAAGCCTTGTCTTACT
+TCAGGCTTCCTAGAAATAGAGCACAAGGCAGGGATTCTTTCTTGCTCGGTGATTTATTGA
+GGAAGTGCTCTCAGAAGAAATTGGTAAGATGCTAAGGAGAACAGCAAAGGACAGGAGAAG
+GGGGCTGAGCAGAGATGGGGATCTAACTGGAATCTGGCCTTTGCTGATTACCAGAGCAGC
+TCTGGGTGCGAATGGTGAAGTGCTGTTCTATTGACAAACTCCACTCAAGTGACATTCCAT
+GCAGCACTGCCAAATTCTGTCCCATAACTCTGCTAGCTCTTCAACAAGAAGTAACTTGAG
+GCAGCACAGTTACAGAAAACAGCACAAGAACCAAGGATACTAAACAGTGACTTAAATGTT
+TTTAGATAAGAGGAAGCAATGAGATACTATAGGGTTTTAATTTCTGTGCAATGGAAAACT
+AGTATTAAATATTTATTAATTAGGAGGAAACGACAATGCTGACTTCTGTCTGCATTATAG
+ACAAAATTGAGTTCTCCAACCATGAGGCAAGGTGCTGGCTTTTTGTACCCCTGCACTATT
+CATTTGATGGGTGAGTGCACTGTAACTTCCAGACGTCTCTTGGTAGGTGGGCCCCACTGG
+CCAAGGGCATTTCCCGGGAGAGTGAACGGCTGTGAGCTACTAGCAGTAGCAGTCACAGCA
+GCTGGGAGGAAACACACTGGTCAGGTAAAGGGCCAGCATCTACCAAGGTCCAGTTCCACA
+ATTAGTGGAGAAATATTTAATAACATTATTTTTGAAAATAATTAGGCCATATGACTTTGA
+CACTTTTTCTCTAGCAAAGTGACTAAAGAGAAGCAGGTTTTTAACTGGGTTTTTATTTCT
+GTTGTGTCTCTAGCCAAAGCCATGCTGATGTTTGATAGTTTTTTTTTTTCTTTTTTTAAG
+AGATGGGGTTTCACCATGTTGGCCATGCTGGTCGTGAACTCCTGACCTCAATGGCCTCCC
+AAACTGTTGGGATTACAGACGTGAGCCACCACGCCCAGCCAGAATTTTTTTTCCTAAAGA
+ATAGAACAACATTATAAAATTTTAGGCATTAAGGACAAATTTTATTTTATGATTTTCATT
+TCGGTGAGTCACAAGATATTCAACACAAAATGAAACTTCACAAAATTTCACAAAATGAAA
+AATTCATTTCAGATTCAATATCCACCTCCATCATCCATATTCATTCTTCCAATGTCTCAG
+GCCAGAAATTTGGAGTATGTGGCTTCTCCACCTCACACAATTTGCCCTAACTTTAATATA
+TACTCAGAAATTACTGGCTTTTCACTGTTTCTATGATTCCCATGTGTAATATACAATACT
+CACCATGCATACAATAATACAATAATTCTGTGTCACAACCACACCTAAATTGGTAAGTTT
+ATAAGGTTATAAGCTGAGAGGTTTTGCTGATCTTGGCTGAGCTCAGCTGGGCAGGTCTTC
+CGGTCTTGGCTGGGGTTCACTGACACACAAGCAGCTGACAGTTGGCTGATCTAGGATGGC
+CTCAGCTGGGATGACAGGCTGTTTCCTCACCTTCCAGCAGGCAAGCCAGTCCCAAGAAAG
+AGAAGGGTGAAACATGGAGGCCATTAATTGAGCCCATCGCATGAAACGCATCTGTGACAC
+CATCACCGTCTGATATCAACTCTCACCTGGATGTTTGCAATCGCCTAACTTTTCTCCTTT
+CATTCACTATGCTGCCTTACAAACCTATTCTCCACAAATCAGCTAGAGCAAACCTTTTAA
+ATCCTAAGTAGAATGCTACCATTCCTCTGCTCAAACTACTGGAGAGGAGATGCCACAGTC
+TTTACTATGGTCTTCAAGACCCTATGGGAGGTAGCCCTGTCTTACAACCATAGCCTCCTA
+CCACTGCCCCAACATGCACACTGAGTTCCGGCCACAGCATCTGCTTCCTCTTTATTGATC
+TGCCAAGGACATGAATGACTCAGAATCTCAAACTTATTCTTCCCTCAGAATCCACTGAGC
+CTACTCCCTCTTTTTCTCAAATGGCAACTTCTCAGAGATGCCTTCTCTGGCTAACGTATA
+TGTACTAAAACCTCCATCCAGCACTCTATGTCATCCTTACTATGGTTTATTTTTCTTCAT
+AGCACCTATCAATTGGTGAAGTATTAAATATGCATTTTTGTTTGTATGCATCTCTCTCCC
+CGCACCAGTATGTGAACTCCACCAGACTGGAGAGCGTGTTTATTTTGTTCACTGCTGTAA
+CTCCAGTGTCTAGAACAGTGCCTGGCACACAGTAGGTGTTTAATAATGATTTGTTAAGCT
+AAGCCAATGAATAAATATTCTTTTGCCCATGAGATGATGTTAAAAATTTTTCAATTATTC
+ATAACTGCCTGTAAGGAATGAATGTTAGTGAATTACTGTGATACCAATGAAAGTTAAATG
+ATGCAATGAAGATTGGGTGGATCACAAGGTCAGGAGTTTGAGACCATCCTGGCCAATATG
+GTGAAACCCCGTCTCTACTAAAAATACCAAAATTAGCTGGGCATCGTGGCAGGACCCTGT
+AGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGGAGGCGGAGGTT
+GCAGTGAGCCGAGATCACGCCACTGCACTCCAGCCTGGCCGACAGAGTGAGATTCTGTCT
+CCAAAAAAAAAAAAAAAAAAGATGTAAATATTATTATTGTTTGCCATCACCCTTATGTGC
+TGTCTTGGCTTTATGTCGTGCTTAGATCTTTTCCAGGTGCAATTTGAATTGATGCAACTA
+ATGGAAACTACAACAGAAGTTCATATTGCCCTATTGTATTACACTATTTGACTCATCTTT
+CAGTATCACCAGGTGCATAAGGAAAATTTCAAAAGTAAATCAAGAGAAAGAAATATGATC
+GCAGCTTAACACAATGTAAATTTATTATTTGTACTTTTTGTCTAAATGGTTTGCCTAAAA
+GACTGAAAGACATTTTATATTAGTTAGAATACTTGAGGATAATAACATAAAAACTTTCCT
+TTCCAACTTGTTTATAAAAGGAAATCTTCACTGTTTTGAACATCAGTTATTTTAAACTTT
+TAAGTTGTTAGCACAGCAAAAGCAACAAAATTCTAAGTGCAGTAATCACTTTACTGCGTG
+GTCATATGAAATCAAGGCAATGTTATGAGTATTACTGGAAAGCTGGACAGAGTAACGGGA
+AAAGTGACTAAAACTATGCAAAACTATGCAAAACTAAGCAGATTGTGTCTCTAGAGTATT
+TCCCATCTCAAGTTTAGTTATTTACTAATTTGGCAACATCTGACCTATCTTTAATTGTGA
+GAAAATAAACAAACACATAAGCCAACTCTCAGAATATGGTTATACATAGGTGTAGCCTAT
+GACTTTGAATGTATTTGTTTGAATAGCGTAAAACAAAATAAAAATAAAATCTTGTTACAG
+TGCAAGAAACGGCAGTCATCAAACTAAGATGAGGCAAGTGTCATGAAGTATGAAAATATG
+GTACCTGAATTCTATTTATTAGAAAGTCTTCACTGAGCTGAGCATGTTTTTTTTAACAAA
+TTCAATTACTGATTTGAATATTTATTATACTTAATTATTGCAGCCATGAAAAGAGGTGCT
+GGCTGAGGCTGCATTTAATAAAAACATTTAATCAGCTTGAGGTTAGTAAACCATTTAATT
+TGTTTTTTCATGAAGATTTAACTTCTAGAATAATTTCATTTATGTATTTTTAGGTATAGC
+CCTAGATTCTGGTCTACATAGTATACAAATCATTTTAGAATGACACTAGGTTATTTCAAC
+TGCTTTTCTACAGAAGTGTTAAATAAGGGAGTAAAGTGTTGGCTTTTTCCATAATTGAAA
+TAAATGCACAATGAGCAGTAACATCCTGATTTCACTGCTATTTTGTTTAATCAACATAAT
+GATGTAGATTTACTCTGTATATATATGGAAGAGTGAAAGAAGGTTGGGAAGGAATAACTA
+TCAATTAATATAGGTGATATAGTAGTTATTTTTGCAAATCAACTATAATTTCTGAATGGA
+TATTCAGACCATATTTACATTACATAGAAGAGGCACACACCAAAAGATTTAACAAATGTG
+CCAAATATTGGTGAATATTTAGTTAGGTACCAAAAGGATGTTGTATAAATTAGGATGCTT
+TCAACCATAAGAGACTCATCTCAAAAATGGCTTGAAAATGTGGGGAATTTTTATCTCAGT
+GTGAAGTTAAAGGTAGGGCAAGTCCAAATCAATTCAAGTTAATTAAAGCCCCAAGTTCTT
+GGAATTTGCTCTGCTAGTCTTAGCTGGTTAGCCTTTGTCCTGAAGTTTGTAACTTCATGA
+CCAGAAGATGATCGCAATATTTTCTAAGTATAAAGCCTGAAGGTGTAAACCAGGTAGTCT
+CAGCAAAACCAATGATGCATGGTCACCTTTCCCTTAGTTGACAAATACTTGCCTTCCAGA
+TACTTTGAATCAGAATGGGCATTTTAACTAAGATCCAGTGCAACTAAAGGAATAATCAAA
+CAAATGATAAAATAATTATTCTGAGCTGAAAACACAAGTCTGAATATTGGAAGAGGTTCC
+TGATTTCCAGGCAGAATAGATAAGCAAAGATATCAACCTAAACACATCCTGGTTATAGTC
+TAAAATTTAGAGAATAAATGGGAAAAGATTATGAACTTTAAGGAAGAAATAACAACTTAC
+ACATAAAACAAAAAGGAAAAACTATCTGTTGACAGATTTATCACCTGCTAGATAAGAGCA
+GAATAACCATTCACTAGGAGAAAATGGGAGAAGCTAGAAGATACTGGAGTAATATTTATA
+GAGTACTGAAGAAAAAACAAAAAACAGAAATTCAATACACAGCTAAGATATCATTTACCT
+GTAAATGATACATGGTAAAATAAAGGGTAAAATAAGGATATTTGCAGATTCACAAGGAGA
+AGTTAGCCTTCACATACTCAGCTGAGGAAAATCCTAGAGACAAAACTCTAACAAAAACAA
+ACTAGCCGGGTGCAGTGGTGCAGGCCTGTAGTTCCAGCTACTCAAGAGGCTGAAGTAAGA
+GGATCACTGGAGCCCAGGGGTTCTGGGCTGTACTGTGCTATGCTGATCAGGTGTCCACAC
+TTAGCTCGCCATCAATATGATGACCTCCCAGGTGGGAAATGGAGCAGGTGAAAACTCCCA
+TGCTGATCAGTAGTGGGATCATGTCTGTGAATAATCACTGCACTCCAACTGGGAAACATA
+GCAAGACCCCATCTCTAAAAAACAAACAAACAAACAAACAAACAAACAAAAATGTTTCAG
+ACAAATGTCAAGATAGAGTAAAAGAAGAAAGTACTGAAGGCCCTTCAACATAAATTGGAT
+CAGATAATAAAAATAATAGCAAAGTTCTTTTCATGCTGTATCCTTAATTCTTCACCATAA
+TCTTAGGAAGTGAATGTATTAATTATCTTTTGCTATATAACAAATTACTCCCAAAACTTG
+GCGGCTTAAAACAACAAATATTATTTCACAATTTCTGTGGGTCAAGAATTTGGAAGTAGT
+GACTCTGGCTCAGGGTCTCATTTAAGGTGGTAGTTCAGGATGCCAGTCAGGGCTGCAGGC
+ACTGAGGCTGCTTCCTCAATGGCCCACTCACATGGCTGTTGGCTGGAGGCCTCTCTTTCT
+CACCACACGGGCCTCTTCATAGGACTGCCCGAGTGTCCTTACAGCGTGGCAGCTGGCTTC
+CCCCAGAGTGAACATTCTGAGAGAGAGAGAAAGAGAGAGTTAGAAGGCATGCTGTCACTT
+CCACTGTATCCCATTCACCAGAAGTGAGAGACTAAATTCACCAAACAGAAAAGTGAAGGA
+GAATGAGGCTCCAGTTTTTTGGGTGAGAGTTGAAGAATGTATGGATATTTTGAACAACCA
+CAATATAATTCTTCTTTTCACAGAAGCACAAAAAAATTTATTTAACTTGTCCAAGTTTAC
+ACAGTTAGCAAGCAACACCTTTGAGAAAAAAATCCATGTAGTCTGATACAAGCACCCAAA
+CTCATAACCACAATGTGAATCTAACTGCTTTTCAATTAAAAAAGAAAGAAAGATTCCCTT
+CAAATCTGGCATATGCATTCACATGGAGCATTCATACTGCCAGTGACAGTACCATAGTTA
+TATGGAATTAGAAGTTCTAACTTATCTTGGCCAAACTAAAGACTTAGGGCTGGGTAGAAG
+GTTGGAGGGATGTAAGGTCATTCTCAAGATCTCATCTAGGAGAAGAAAACAAAATGGGGA
+AGTAGAAGACAAAATGCTTTTTTAGGTTGGGAAAGGACTGGGAGAATCAAGCATCTAGAA
+ATGGGCACAAAGAGTTACCTTATTTTATTTAAAAGAAAATAAATGTTTGACTATTAATGC
+CTGAGAACGGAAGGTGATTATTAATGAGATGAAAAAGTTAATCAGATTCTCCAAGTTAGG
+AGGGACTTGAAGACCAAATTGATAAAAATAAAAAAAAAGATGTCATAGTAGAATAATCTA
+GATAATAAGCAATCAATGAGACTGAAAAAATAAAATCAAGTATATCATTTGTTACACTAA
+ATATTAATATACCAGATTCTCTCATTAAAAAAACAGAGAAAGTCAAATTGGATTAAATAA
+GAACAAAAAGTTAGCTATATAGTATTTATCAGAAACATTCTTATAAACAAATTGATAATG
+AAAGATTAAAAATAAGAGATTTGAGGCAAGGCAAGCAAAAAGAAATAAATGTTAAACAAG
+GAGAAATTAAAGGCTACGGACATTACCTAAGGAAAAGGATGACATAGAGTTACAGTGGCA
+AAAGTTAGGAAGCAGATGACATAAATCTATATGCACAAACAGTATGGCCACAAAATACAT
+TAATTAAAAATTACTAGAAATATAAGATGACTTTGATTAAAATACACTGATTACAAGGGA
+TTTAACATATAAAAATTAGGCTGATGTGGTAAATTTAAATATAATCAAATATTTAGGAAA
+ATAGAACAACACAACAAAGTTGATTACATATATTCATTTTCCAGATAGTATACTTTATGC
+CTATGAAATAGTTCTTAAAATCAATTATATATGGCCGGGTGCAGTGGCCCACGCCTGTAA
+TCCCAGCACTTTGGGAGGCCAAGGCAGGTGGATCACGAGGTCAGGAGATCGAGACCATCC
+TGGCTAACACAGTGAAACCCCGTCTCTACTAAAAATACAAAAAAAAAAAAAATTAGCTGG
+GCGTGGTGGCTGGAACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT
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1 src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.subset.fasta.fai
@@ -0,0 +1 @@
+20 9000 4 60 61
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2 src/test/resources/htsjdk/samtools/cram/test.dict
@@ -1,2 +0,0 @@
-@HD VN:1.4 SO:unsorted
-@SQ SN:Sheila LN:20 M5:7ddd8a4b4f2c1dec43476a738b1a9b72 UR:file:/Users/edwardk/Documents/htsjdk/testdata/htsjdk/samtools/cram/auxf.fa
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2 src/test/resources/htsjdk/samtools/cram/test.fa
@@ -1,2 +0,0 @@
->Sheila
-GCTAGCTCAGAAAAAAAAAA
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1 src/test/resources/htsjdk/samtools/cram/test.fa.fai
@@ -1 +0,0 @@
-Sheila 20 8 20 21
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2 src/test/resources/htsjdk/samtools/cram/test2.dict
@@ -1,2 +0,0 @@
-@HD VN:1.4 SO:unsorted
-@SQ SN:Sheila LN:20 M5:7ddd8a4b4f2c1dec43476a738b1a9b72 UR:file:/Users/edwardk/Documents/htsjdk/testdata/htsjdk/samtools/cram/auxf.fa
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2 src/test/resources/htsjdk/samtools/cram/test2.fa
@@ -1,2 +0,0 @@
->Sheila
-GCTAGCTCAGAAAAAAAAAA
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1 src/test/resources/htsjdk/samtools/cram/test2.fa.fai
@@ -1 +0,0 @@
-Sheila 20 8 20 21