Adds support for base quality recalibration for BAM files
Adds support for base quality recalibration for BAM files
Fixed recalibrate tool arguments name
Added prototype for region extraction from CIGAR in indel realignment
Added alignment region intervals generation
Old alignment region file deleted
Added source files for auxiliar alignment related functions
Added source files for local indel realigment functions. Implemented cigar unclip and M count.
Added first implementation for leftmost indel alignment
Bugfix
Removed .o files from repository
Fix: Minor bugs in recalibration argument parsing
Added realign command to hpg-bam
Added help line for realign command
Added realigner launcher file for execution from hpg-bam
Fix: Memory leak fixed in alig_bam_batch function
Added compilation parameters for realign command
Added more than one batch processing
Added CIGAR aligned counter to alig.c
alig_cigar_leftmost now returns original cigar if its length is >= 30