Fixed bug loading transcriptome file
Fixed bug in output file name when the option --prefix is present
Adds some output messages for large genomes not supported
Changes CHROM table form char to unsigned char
Warnings with -Wall fixed
Fixes insertion bug
Adds merge_seeds function
Fixes one seed
Fixes some CIGAR codes
Merge branch 'develop-2.0.1-beta' of https://github.com/opencb/hpg-aligner into develop-2.0.1-beta
Removes some debug messages
Updates submodules
Fixed conflicts in submodule
Updates submodule
Updates submodule
Improves mapping by processing read flanks (start and end)
Fixes some CIGARs
Remove some files from Git and fixe one bug in sa_mapper_stage.c
Fixed conflicts in merge with develop-2.0.1-beta
Updates submodules