SCMO 0.1.12

All barcode files now start at index 1
BamTabulator: show available tags and pysam attributes
Added -max_handles setting to bamSplitByTag.py
Index bams using multiple threads
Added overseq count table generator
Extended help and added blacklist argument
Added functions to read and write blacklist to bam file header
Added timeout args
Write blacklisted regions to bam file
Change default strand inversion value
Use -p flag for samtools merge to prevent PN: dupes
Fall back on calling samtools binary, it works better with -c -p flags
Added gitignore folders
Added XA filter to bamFilter
Check validity of —contexts_to_capture
Fixed taps strand parameter bug, set taps strand default to R
Fix out of range error when using contexts_to_capture and molecule is on start of contig