htsjdk
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samtools
A Java API for high-throughput sequencing data (HTS) formats.
@tfenne a rough implementation of https://github.com/samtools/htsjdk/issues/793. I can probably make the function itself faster. Related to https://github.com/samtools/htsjdk/issues/793
The `accumulator` field is used with the following access patterns: - .remove(0) - .add(element) - .add(0) - .sublist(0,i).clear() - .get(0) - .get(i) as one can see, except for the last...
Hello, I've searched around a bit to see if there is a simple answer to my problem (like #722) but could not seem to determine what performance hits people are...
TabixReader parseReg method assumes these characters don't appear in sequence names. This came up in the review for https://github.com/samtools/htsjdk/pull/911.
Some exciting news! The Methods team at Broad recently applied for, and were subsequently awarded a [grant](https://chanzuckerberg.com/eoss/proposals/htsjdk-enhancing-the-java-toolkit-for-emerging-sequencing-technologies/) as part of the [Chan Zuckerberg Initiative’s Essential Open Source Software Program](https://chanzuckerberg.com/rfa/essential-open-source-software-for-science/) to...
Right now, only 1 thread per file is used. Compression easily has enough work for multiple threads and it would speed up the runtime
The VCF parser is currently unable to parse VCFs with complex rearragnements and this is showing up as Picard issues: https://github.com/broadinstitute/picard/issues/1406 Need to prioritize and fix.
Users who are using FUSE to access remote file systems are having trouble with the bam index memory mapping. I've been told that exposing the ability to specify the PRIVATE...
The CRAM huffman tree implementation assumes that a codeword will fit in 32 bits. The code detects and rejects codeword lengths that exceed the limit, but there should be an...
### Description * Clean up a bit the code. - Removed per value switches. - String, character initialization. * Optimize some operations - Fast look-up of values from primitive codes....
