Convert HapCUT2 to use the HTSlib API instead of the legacy samtools API #87
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Change to include htslib/*.h headers; use HTSlib-style type and function names; use sam_hdr_read() and pass bam_hdr_t headers explicitly to sam_read1(). Remove references to libbam.a and don't build it. The only remaining use of submodules/samtools is in the install-samtools rule. Use HTSlib's kseq.h instead of a local copy.
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This pull request converts the hairs-src/*.c source code to use HTSlib for its BAM-reading needs rather than the old samtools 0.1.x API. The old API has been unmaintained for many years and this means that the code needs only HTSlib, not HTSlib and Samtools.
This compiles against just HTSlib (both 1.2.1 and the current release), but I have not tested it or even tried to run it.
With this change, the only reference to the samtools submodule code is in the
install-samtoolsrule. If you changed this to a README recommending installing a current Samtools, you could remove the samtools submodule entirely.This also paves the way to building HapCUT2 against current HTSlib instead of 1.2.1 — which is now almost 5 years old.