htsjdk

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Truncation issue with GZIPInputStream when reading bgzip-compressed streams

2

### Description of the issue When reading bgzip-compressed data from a stream (e.g. over the network or from a pipe), htsjdk can stop early and not read the stream all...

jkmatila

Trying to add an http nio provider as a test dependency as part of #1688 caused issues because of some deficiencies in the library. See the [test results here](https://github.com/samtools/htsjdk/actions/runs/6511698941?pr=1688) There...

lbergelson

Make AbstractVCFCodec thread-safe, allowing for multi-threaded VariantContext genotype decoding

3

### Description **Problem:** Processing multiple `VariantContext` objects concurrently results in shared data due to the stateful nature of `AbstractVCFCodec`. Internal data structures (`parts`, `genotypeParts`, `alleleMap`, `lineNo`) are re-used to parse...

rcoleb

### Description of the issue: For "multiallelic" sites containing a spanning deletion alleles (represented by `*`), the `getType` method in `VariantContext` behaves somewhat unexpectedly. There have been numerous old discussions...

rickymagner

I have posted this request over in htslib, but was just informed that for IGV what matters is htsjdk instead ... https://github.com/samtools/htslib/issues/1440 I might be able to motivate Microsoft to...

smrgit

It looks like I introduced a bug in `IOUtil.openFileForMd5CalculatingWriting()`. It appears to resolve `filename/.md5` instead of `filename.md5`. We never noticed because it doesn't have tests.

lbergelson

Add a better error message when the reference is too long for indexing

5

There have been two seperate issues this week with people running into a confusing indexing error when using a long reference. We should give a better error. We should ideally...

lbergelson

Hello all, I was trying to organize some of the permissions for htsjdk since there are a lot of people with write access who no longer are active / employed...

lbergelson

SAMFileWriterFactory creates .bai file when writing .cram file

1

### Description of the issue: When using the `SAMFileWriterFactory` to write a .`cram` file, when the "create index" default is toggled on, it will create a `.bai` file for the...

rickymagner

Partially missing AD and PL are treated as empty

5

As part of reviewing https://github.com/samtools/htsjdk/pull/1372 I noticed that if we parse an AD or PL field in a vcf that has a missing value as one element (ex: `10,.,5` *edit:this...

lbergelson