Can I read chrom, strand, pos, len from bam files without htslib?

Question

[Click downvote]

I am having trouble compiling my program when I use htslib. Since this is software many other people are likely to use, I imagine my pain * 10000. Is there a way to read bam files without htslib? I just need the chrom, start, end and strand.

Otherwise, is there a way to include all of htslib in my software?

I am using the bioconda htslib and the flag -Ihtslib when compiling, but I get the error:

fatal error: htslib/sam.h: No such file or directory
 #include "htslib/sam.h"
          ^~~~~~~~~~~~~~

Answer 1

[Pierre Lindenbaum]

-Ihtslib means there is a directory named htslib in your current directory and this directory a bunch of *.h files.

if this directory is not in the current working directory , search for it (someting like)

find / -type -f -name "sam.h" 2> /dev/null

(wait if you have a large server). Then use

-I/path/to/the/directory/htsdlib

I am using the bioconda htslib

does it contains the sources of htslib ? try to install htslib from github without conda

[John Marshall]

HTSlib's headers are set up so that they are in an htslib/ subdirectory of an includedir and used with #include "htslib/sam.h" etc. This avoids collisions with other libraries that might provide unrelated headers coincidentally named sam.h.

So if your find command shows /path/to/the/directory/htslib/sam.h, the -I option you should use will be -I/path/to/the/directory.

[Click downvote]

So I can include the whole htslib-project in my project if I want other users to compile easily?

[Pierre Lindenbaum]

So I can include the whole htslib-project in my project

what does 'include the whole htslib-project in my project ' means ? are you talking about git submodules ? https://git-scm.com/book/en/v2/Git-Tools-Submodules

[Click downvote]

I want people to not need to have htslib installed when they compile my software. So I can have a folder with htslib in my codebase and point to it.

[Alex Reynolds]

You can: It is MIT-licensed. https://github.com/samtools/htslib/blob/develop/LICENSE

Answer 2

[endrebak852]

My solution. Works, but probably not the cleverest. Hinges on users having conda w/appropriate libs installed:

# In setup.py
from subprocess import check_output

conda_path = check_output("which conda", shell=True).decode().strip()

conda_include = []
conda_lib = []
if conda_path:
    conda_base = conda_path.replace("bin/conda", "")
    conda_include.append(conda_base + "include/")
    conda_lib.append(conda_base + "lib/")

extensions = [Extension("bla.src.reads_to_bins",
                        ["bla/src/reads_to_bins.pyx", "bla/src/gzstream.cpp"], language="c++",
                        include_dirs=conda_include,
                        library_dirs=conda_lib,
                        extra_compile_args=compile_options,
                        libraries=["z"]),

Chapter 7 of Computer Systems: A Programmer's Perspective was of great help. The book is highly recommended for people who want to understand computers from a C programmers perspective.