Questions tagged [htslib]
8 questions
3
votes
1 answer
Is it possible to do Rcpp::wrap without copying for a very large std::vector
I have an Rcpp function that reads large BAM file (1-20GB, using htslib) and creates several very long std::vectors (up to 80M elements). The number of elements is not known before reading, so I cannot use Rcpp::IntegerVector and…
notch
- 49
- 5
2
votes
1 answer
How can I load C++ modules and include compilation flags as a part of Rcpp package compilation?
I am using Rcpp to wrap a C++ program in an R package. My C++ program requires the following header:
#include "htslib/sam.h"
Prior to compilation, I typically load the following module in Ubuntu:
HTSlib/1.11-GCC-9.3.0
I typically compile the C++…
annabelperry
- 53
- 5
1
vote
0 answers
Docker installation testing fails because of missing dependency which was installed earlier
I'm trying to create a deb of a python project for Ubuntu 18.04 via docker which passes installation testing.
My compile.dockerfile includes this:
RUN apt-get update && \
apt-get install --yes --no-install-recommends \
zlib1g-dev \
libbz2-dev…
azural
- 21
- 3
1
vote
1 answer
How to extract genotype information for each sample as a string from a VCF file using htslib?
I am using htslib for extracting all the information contained in a VCF file in C++.
Currently, thanks to the VCF specification and the documentation in the file vcf.h, I have successfully extracted all the metadata information in the header…
Alberto Casas Ortiz
- 806
- 3
- 23
1
vote
1 answer
Use Htslib for VCF files extracting alternative allele information
I am working with c++ to handle VCF files, to do this I use a vcf library from htslib (https://github.com/samtools/htslib/blob/develop/htslib/vcf.h). I know there might be some better libraries, but I'm also working with other file formats for which…
RAHenriksen
- 143
- 2
- 12
0
votes
0 answers
Dockerfile issue when running autoheader command - "Can't locate strict.pm in @INC"
I'm working on my first dockerfile and trying to install htslib but I get the following "can't locate strict.pm" error. Does anyone know what this could be or how to fix it?
---> Running in 0fd66f94ef7c
+ mkdir -p /opt
+ cd /opt
+ ls
aws
+ git…
0
votes
1 answer
Unable to install htslib v1.12 with conda
I could not install htslib v1.12 with conda using either commands:
conda install -c bioconda htslib
conda install -c bioconda/label/broken htslib
Using conda install -c bioconda/label/cf201901 htslib gave me htslib v1.9.
Does anyone know how to…
Ngân Trần
- 3
- 1
0
votes
0 answers
How to properly link to a C library in cython C++ build
I have a compiled C library htslib in my module top-level directory, this is first built using ./configure; make outside of python before running python setup.py install. I am trying to use headers listed in htslib. I have cython scripts e.g.…
kezzos
- 3,023
- 3
- 20
- 37