htslib
htslib copied to clipboard
samtools
C library for high-throughput sequencing data formats
See Will Stokes' request at https://sourceforge.net/p/samtools/mailman/message/36454348/ We desire a way to construct a BAM record from the component pieces that isn't just a manual mess of bit/byte shuffling. Most of...
To reproduce, build HTSlib with @jkbonfield 's malloc testing framework. Create a small cram file: ``` FUZZ=1000000 ./test/test_view -C -t test/ce.fa test/ce#1000.sam > /tmp/ce#1000.cram ``` Try to read it back,...
Hi there, according to the VCF Spec 4.2, > For one individual, **each integer** in the vector is organized as `(allele + 1)
This is a variation/duplicate of https://github.com/samtools/htslib/issues/664, which I could not re-open, hence please excuse to start a new issue here. The above issue handles the case of setting variable length...
We can now count the depth anywhere along the read rather than only at the left end. It's not buffering reads up so it doesn't know what's about to come,...
Hi, We still need "wbu" mode for pipe output, such as bwa | samtools fixmate | samtools sort but now 'samtools view -u ' is changed from 'wbu' to 'wb0',...
If we're reading and writing VCF without intervening change to BCF or use of bcf_unpack with BCF_UN_FMT (so no querying and/or modification of the per-sample FORMAT columns), then we keep...
OS Ubuntu 18.04 (within a docker container) htslib v1.10.2 compiled from source (also when installed from the v0.7 apt package) gcloud SDK v235.0.0-0 installed from apt package We have a...
1. The new method `sam_open_write` can open a `htsFile` file in writing mode only, attach a header struct (`sam_hdr_t`) to it and write the header data to the disk, before...
Hello I am trying to install htslib-1.3.1 on Ubuntu 12.04 using ./configure and make but getting the following error message. Also I have verified that zlib1g-dev is installed and up...
