Bam t

[masarunakajima]

• 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