Related Issues (20)
- 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 4
- SAMFileWriterFactory creates .bai file when writing .cram file HOT 1
- Deleted Java developers team
- support for Azure blob storage? (specifically access to BAM/CRAM files in Azure blob storage by IGV)
- VariantContext has inconsistent behavior on getting allele type with spanning deletions
- Resolve issues around integrating HTTP NIO provider
- Truncation issue with GZIPInputStream when reading bgzip-compressed streams HOT 2
- Ambiguous assertions in the tests HOT 1
- Iterator not working on vcffileReader HOT 3
- Incomplete license metadata in build.gradle
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