Add a large CRAM roundtrip test and samtools rountdtip test.

samtools · May 14, 2024 · 64180f8 · 64180f8
1 parent f276317
commit 64180f8
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Showing 2 changed files with 5 additions and 8 deletions.
diff --git a/src/test/java/htsjdk/samtools/CRAMAllEncodingStrategiesTest.java b/src/test/java/htsjdk/samtools/CRAMAllEncodingStrategiesTest.java
@@ -27,19 +27,16 @@ public Object[][] defaultStrategyRoundTripTestFiles() {
                 { new File(TEST_DATA_DIR, "NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram"),
                         new File(TEST_DATA_DIR, "human_g1k_v37.20.21.1-100.fasta"),
                         false, false },
-                { new File(TEST_DATA_DIR, "NA12878.20.21.1-100.100-SeqsPerSlice.0-unMapped.cram"),
-                        new File(TEST_DATA_DIR, "human_g1k_v37.20.21.1-100.fasta"),
-                        false, false },
-                { new File(TEST_DATA_DIR, "NA12878.20.21.1-100.100-SeqsPerSlice.1-unMapped.cram"),
-                        new File(TEST_DATA_DIR, "human_g1k_v37.20.21.1-100.fasta"),
+                { new File(TEST_DATA_DIR, "CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram"),
+                        new File("src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz"),
                         false, false },
                 { new File(TEST_DATA_DIR, "NA12878.unmapped.cram"),
                         new File(TEST_DATA_DIR, "human_g1k_v37.20.21.1-100.fasta"),
                         false, false },
-                { new File("src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram"),
+                // generated with samtools 1.19 from the gatk bam file CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam
+                { new File(TEST_DATA_DIR, "CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram"),
                         new File("src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz"),
-                        false, false },
-
+                        true, false },
                 // these tests use lenient equality to only validate read names, bases and qual scores
                 { new File(TEST_DATA_DIR, "mitoAlignmentStartTestGATKGen.cram"),
                         new File(TEST_DATA_DIR, "mitoAlignmentStartTest.fa"), true, false },

diff --git a/...est/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram b/...est/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram