Fix one bug in options.c
Creates a new seed structure for SA in order to contain statically the cigar structure (the idea is avoid making many small mallocs)
New Gzip fastq pe reader, revcomp in fastq structure and reader gzip implemented
Add PE mode to DNA and permit run with more than one fastQ files
Computes CIGAR code for seeds, and extends seeds first to the left-side, and then ,to the right-side (for an efficient CIGAR generatiion)
Resolves conflicts
Improves the main funcion in hpg-aligner.c
Computes a score for each CAL
Add argtable to index_builder.c/h
Fix conflicts from 'jtarraga'
Nothing...
Resolves some conflicts
Merge branch 'develop-rna' of https://github.com/opencb/hpg-aligner into develop
Resolves some conflicts and frees some memory
Delete some 'printfs' for debuggin
Merge branch 'develop' of https://github.com/opencb/hpg-aligner into develop-rna
Move 'options_free' to 'hpg-aligner.c'
Merge branch 'develop' of https://github.com/opencb/hpg-aligner into develop