Samtools Htslib Issues

Issue Title State Comments Created Date Updated Date How to get a specific chromosome
open
1 2022-07-14 2022-07-18 tabix returns row from VCF file multiple times
open

4 2022-07-11 2022-07-18 Modified base parsing failure failure
closed
0 2022-07-01 2022-07-18 extract genotype information
open
1 2022-06-24 2022-07-18 sam_hdr_remove_lines is inefficient if original header contains a lot of lines
open
1 2022-06-23 2022-07-18 issue when trying to use htslib
closed
3 2022-06-23 2022-07-18 bcf_set_variant_type does not correct set type BND for reverse strand breakends
closed
0 2022-06-16 2022-07-17 Extend vcf.h API to distinguish between the two indel types
open
1 2022-06-14 2022-07-14 Feature request: extend mpileup API
open
2 2022-06-14 2022-07-14 An error ” Could not write 32768 bytes: Error 0″ while running bgzip
open
0 2022-04-23 2022-04-18 Random read error on google cloud.
open
4 2022-04-21 2022-07-15 htslib 15.1 version
closed
2 2022-04-11 2022-04-18 Support optional `.` and `?` in Mm tag
closed
3 2022-04-05 2022-04-18 Index of aux tag in sam/bam record
closed
6 2022-04-02 2022-07-11 Samtools can no longer write BAM files with more than 2GB of headers (since v1.10)
closed
1 2022-03-15 2022-04-18 failed to use libdeflate in htslib
closed
3 2022-03-10 2022-04-18 [E::hts_idx_push] Chromosome blocks not continuous for gnomad.tsv.gz
closed
2 2022-03-09 2022-07-12 tabix: unexpected behaviour at “coordinate” 0 and with 0-based indexing
closed
3 2022-02-24 2022-04-18 Samtools MPileup : [E::Incorrect %s tag type (%c) for read %s]
closed
3 2022-02-21 2022-04-18 Feature Request: Expose the total length of a contig
closed
1 2022-02-21 2022-07-01 CRAM with relative path to reference
closed
2 2022-02-16 2022-04-18 Questions concerning the sam/bam/cram functionality
closed
3 2022-02-14 2022-07-01 hts_log_error() extension for better error reporting
open
5 2022-02-14 2022-06-29 hts_parse_decimal() silently fails on non-numeric strings starting with G
closed
2 2022-02-11 2022-04-18 bgzf_seek fails for seeks > 65296?
closed
5 2022-02-03 2022-04-18 bgzf_seek doesn’t work on native gzip-generated files
closed
7 2022-02-03 2022-04-18 Incorrect count of unmapped reads in a CRAM file using samtools view
closed
5 2022-01-25 2022-04-18 Interface with htslib.a
closed
2 2022-01-25 2022-07-12 The unauthenticated git protocol on port 9418 is no longer supported
closed
3 2022-01-11 2022-04-18 [Documentation] Short examples?
open
1 2022-01-01 2022-07-08 Some erros occured during make ! such as undefined reference to `regcompA’
closed
3 2021-12-20 2022-04-18 Unchecked return values of pthread_mutex_lock
closed
3 2021-12-14 2022-04-18 FASTQ can be parsed faster
closed
5 2021-12-09 2022-04-18 bcf_sr_seek() still fails
closed
6 2021-11-30 2022-04-18 Confusing BCF error messages, and mixing warnings vs errors.
open
7 2021-11-11 2022-04-18 vcfutils::bcf_remove_allele_set should unpack to BCF_UN_INFO
closed
6 2021-11-05 2022-04-18 Fix indexing bug with “placed” unmapped reads.
closed
10 2021-11-03 2022-04-09 how to get the value attached to “PU” and “SM” in @RG line of a sam header using htslib ?
closed
2 2021-10-29 2022-04-18 tabix fails to open bed with multiple columns
closed
2 2021-10-27 2022-04-18 Compiler error in htscodecs.c
closed
3 2021-10-16 2022-07-16 Add basic recognition for XZ- & Zstd-compressed data, and D4 format
closed
7 2021-10-05 2022-01-26 Feature request: Add option to tabix to interleave multiple bgzipped indexed files, without the need for external resorting.
open
9 2021-10-04 2022-04-18 Failed to locate HTSLib on your system. HTSLib library and headers can’t be found.
closed
9 2021-09-21 2022-04-18 Move the “start<1” error check in cram_get_ref to before thread locking.
closed
0 2021-09-15 2022-02-10 Improper locking bugs(e.g., deadlocks) on the lock
closed
6 2021-09-14 2022-04-18 Modified bgzf EOF warning to make it less alarming.
closed
0 2021-08-17 2022-01-23 Error while loading shared libraries
closed
0 2021-08-15 2022-07-17 Pair lines with symbolic alleles by END tag
closed
0 2021-08-12 2022-02-02 Wish list: aux tag iterator API
open
0 2021-08-10 2022-07-13 htslib version update
closed
2 2021-08-10 2022-03-15