htsjdk
htsjdk copied to clipboard
samtools
A Java API for high-throughput sequencing data (HTS) formats.
### Description of the issue: When calling assertFilesIsWritable through htsjdk.samtools, through Picard mark duplicates, we find that IOUtil.java fails to correctly assert writable on NFS file shares that have special...
According to the VCF 4.3 specification, spaces are allowed in INFO field values (unlike in VCF 4.2). However, trying to parse such a file fails with an error message "The...
Currently `SamReaderFactory` stores a DEFAULT factory as a static variable. Certain operations update this default so when `SamReaderFactory.makeDefault()` is called it returns different values. However, some default values are set...
I recently used htsjdk 3.0.5 to complete my own project, I would like to ask how htsjdk needs to be used to generate fai files and tbi files, thank you
Hi all, here is a proposal for a new package `htsjdk.tribble.gtf` ### Description htsjdk contains a gff3 codec but is still missing a GTF codec. I wrote a few classes...
### Description of the issue: Is it possible to use the 8-Bin Base Quality Compression with the new overhauled CRAM support in 3.0.5? #442 indicates that this would be possible...
Edit 14/03: verified that this also occurs in version 3.0.4 ### Description of the issue: When I add a header including a description containing escaped double quotes, sometimes the "escape...
### Description of the issue: Converting a SAM file to a BAM file was slower than expected. When looking at the profiler i noticed the following:  The SAMReader uses...
### Description of the issue: Using the Histogram methods to get values when the histogram is empty are implemented in an unsafe way, leading to unhelpful error messages in some...
Hi all, just a question about the API. I want to scan a vcf.gz and it's tbi to extract the min/max variant.POS for each contig. I'm not sure if I...