BAM: Deleted obsolete functions in alig.c/h
Fix bug in options
Change default output dirname and handle output filename for SA
[BAM]Fix: cigar32_create_ref function now handle clips S-H-P correctly (for now)
[BAM]Fix: new_sequence_from_bam_ref now writes end character 0 in the end of generated string
[BAM]Implement: Added reference reading from genome_t to alig_bam_list function
Improves timing support for SA (using #ifdef _TIMING), and updates submodule hpg-libs)
Merge branch 'develop' of https://github.com/opencb/hpg-aligner into align
[BAM]Implement: Functions for reclipping a cigar and get indels structure from cigar
[BAM]Implement: Haplotype correct extraction from interval list with reads in realignment
Merge branch 'develop' of https://github.com/opencb/hpg-aligner into develop
Merge branch 'align' into develop