Fixes some typos
Adds input parameter --num-seeds, and it uses read->revcomp for the reverse strand
Adds some counters, improves the create_alignments function,...
Groups SW by batch in order to take advantage of the SSE Smith-Waterman
Updates submodule hpg-libs
Improves CIGAR codes
Fixes some CIGAR codes by using X, = characters instead of M character, and fixes some memory leaks
Fixes the SA index creation and comments some counters
Adds a function to support pairs and improves the exact read handling
Resolves conflicts
Adds the --bam-format parameter to save results in BAM format, and it prepares support for realignment and recalibration
Updates submodule lib/hpg-libs
Merge branch 'develop' of https://github.com/opencb/hpg-aligner into develop
[BAM]Fix: Bugfixing