Add support for reading SAM, BAM, CRAM, BCF, VCF with multiple thread…

[ghuls]

…s.hts_set_threads

Add support for reading SAM, BAM, CRAM, BCF, VCF with multiple threads
by using hts_set_threads().

[ghuls]

# count_reads_in_bam.seq 
from bio import *
from time import timing

bam_filename = 'ENCFF014BMO.bam'


def count_reads_in_bam(bam_filename, nthreads):
    nbr_reads = 0

    for r in SAM(bam_filename, nthreads=nthreads):
        nbr_reads += 1
        #print(r.name, r.read, r.pos, r.mapq, r.cigar, r.reversed)

    return nbr_reads

# Warmup cache.
count_reads_in_bam(bam_filename, 4)

for nthreads in [0, 1, 2, 3, 4, 6, 8]:
    with timing(f"Read BAM file with {nthreads} threads:"):
        print(count_reads_in_bam(bam_filename, nthreads))

seqc run --release count_reads_in_bam.seq 
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Read BAM file with 0 threads: took 9.35422s
15707047
Read BAM file with 1 threads: took 6.34794s
15707047
Read BAM file with 2 threads: took 3.98488s
15707047
Read BAM file with 3 threads: took 3.93837s
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Read BAM file with 4 threads: took 3.96835s
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Read BAM file with 6 threads: took 4.01037s
15707047
Read BAM file with 8 threads: took 3.94179s