htslib
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samtools
C library for high-throughput sequencing data formats
I'm trying to remove the VCF header line for a symbolic alternate allele. Since `##ALT` header lines belong to a specific BCF_HL_* type, it seems like my only options are...
While looking into samtools/samtools#712 I've discovered an input to probal_glocal() that makes it return a negative value. Unfortunately, the return value from probaln_glocal doesn't seem to be documented anywhere, but...
Hi, I was wondering if there has been any discussion around extending bgzip/tabix to support BEDPE files (to ultimately achieve 2D block-compression + retrieval). Useful for Hi-C interaction matrices, SV...
When htslib reads a BAM record, if there is no cigar string the 'unmapped' flag is set and a warning message sent to stderr. This is contrary to the SAM...
Here's a few correct VCF files from a bioinformatics [tiny-test-data](https://github.com/brainstorm/tiny-test-data) repository: ``` $ find . -iname "*.vcf" ./sample1-bcbio-cancer.vcf ./sample2-bcbio-cancer.vcf ./spec-svs-v4.1.vcf ./spec-v4.3.vcf ``` Using `xargs` to bgzip all the files in...
The _cram/_ subdirectory has various items that are a legacy of its iolib origins, and as a part of htslib could be recoded using existing HTSlib facilities instead. * _cram/zfio.c_...
Would it be possible to make htslib's error reporting optional, perhaps in the form of a preprocessor directive? I'm writing an application which makes heavy use of htslib, and would...
(via pysam) A VCF that has repeated sample names causes htslib to crash. An offending VCF can be found here: https://github.com/ga4gh/server/tree/master/tests/faultydata/variants/duplicated_sampleid . As described here: https://github.com/ga4gh/server/issues/521
Add a flexible array member to the bam1_t struct to allow the variable-length data to be colocated in memory with the rest of the bam1_t. This should be backwards compatible,...
This is partly to replace the c-maint repository and additionally to add the ability to validate the tar balls is constructed correctly by unpacking, building and testing.
