Modified BamReader::read_entry to use bam1_t directly instead of converting it to string.
Fixed the problem of ending quality score parsing two bases short for bam files.
Created mechanism to skip quality score parsing if no quality scores are given, for sam and bam files
Made a function to make sure the vectors in tile_position_quality and tile_position_count all have length of maximum read length. This is needed for sam and bam files because the lengths of these vectors remain 0 if quality score parsing is skipped by the above mechanism.
Made separate cases for bam and sam in get_tile_split_position
BamReader::read_entry
to usebam1_t
directly instead of converting it to string.tile_position_quality
andtile_position_count
all have length of maximum read length. This is needed for sam and bam files because the lengths of these vectors remain 0 if quality score parsing is skipped by the above mechanism.get_tile_split_position