vasudeva8
vasudeva8
Fixes #1735. Added option to provide number threads to use, disabled by default. Uses the thread pool in operations except listing of sequence names (-l).
Samples updated with fasta/fastq index using, tabix index and thread pool queueing of tasks.
fixes #2055 fasta/fastq output of faidx/fqidx will be bgzf compressed if the output file has an extension of .gz/.bgz/.bgzf. stdout will not be compressed. also added extended option output-fmt-option to...
faidx/fqidx index can be created along with sequence retrieval, with --write-index option uncompressed output was created through FILE handle and updated to create using BGZF uncompressed writing fqidx man page...
Reserved format field CICN was added in VCF v4.4 (vcf v4.4, 28-Jun-24) and yet to be added to 4.4 List of changes. Also the relation between format field CI and...
VCF v4.3 - v4.4 changes (section 7.2 in spec v4.4,28-Jun-24) mentions that “Number, Type and Description required only for INFO meta-information lines“. This contradicts to what described in section 1.4.4...
This is a draft, to fix https://github.com/samtools/samtools/issues/2238 htsFile updated to hold extra data, when max depth check is enabled. The max depth check is set using input-fmt-option, seq_max_depth. Extra data...