Comments (3)
nh13
commented on June 17, 2024
@kshakir can you make a pull request?
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kshakir
commented on June 17, 2024
Sure, but not 100% sure how you folks want this done.
Option a) refactor the BAM code a bit, making things like isValidFile() more general use or b) continue in the path of this duplicated code and copy and paste the checks into the current isCRAM()?
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jacarey
commented on June 17, 2024
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Related Issues (20)
- LittleEndianInputStream EOF test is incorrect HOT 9
- EdgeReadIterator (used in Picard's CollectWgsMetrics) doesn't handle intervals correctly HOT 2
- IntervalTree.Node's methods have package visibility only HOT 1
- What is the non-deprecated replacement for acceptableAlleleBases? HOT 4
- Our FastaSequenceIndex too large to fit in memory HOT 4
- The last-but-one argument of test testQueryAlignmentStart in HtsCRAMCodec30And21QueryTest.java is long HOT 1
- CRAM files have zero-length blocks with a compression method associated with them (so cannot be decompressed). HOT 1
- VCF sorting change breaks existing VCFs HOT 1
- Race conditions accessing CRAM's reference data through ReferenceSource
- Add a better error message when the reference is too long for indexing HOT 5
- Question: Tabix index to find min(POS) and max(POS) in each contig
- Histogram class uses unsafe methods for returning min/max
- CRAM: 8-Bin Base Quality Compression HOT 1
- SamReader slower than expected on network drive HOT 1
- Escaped doublequotes in INFO descriptions result in invalid VCF file HOT 2
- Question: How to generate FAI files and TBI files HOT 5
- SamReaderFactory should use current defaults when makeDefault() is called
- Error when reading a VCF 4.3 file with spaces in INFO field values HOT 1
- htsjdk.samtools.util.IOUtil.assertFileIsWritable on certain NFS environments fails to correctly assess permissions HOT 1
- SAMFileWriterFactory creates .bai file when writing .cram file HOT 1
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