Update makefile
Update markduplicates to support mixed alignments
Experimental mixed/discordant alignment support
tmp_reads weren't being updated
At least bison_herd seems to now work
Forgot to reset some pointers
Have bison_herd keep track of concordant/discordant/singleton metrics
Remove debugging printf
Fix XS tag
Without --no-mixed, there's no guarantee that reads are received #1 then #2. We now check for this and send them in the correct order if not.
Fix bit comparisons used to distinguish discordant from singleton alignments
Prevent throttle-induced deadlocks due to comparing total pairs and total individual reads
Fix memory leaks in bison_index
Fix small memory leak in read_genome()
Fix various memory leaks
Fix single-end mapping
Remove some debugging stuff
Change mtid and mpos as needed
Update mpos on read#2 if read#1 is unmapped
Fix an apparent bug in (sometimes) trimming CTOB reads during methylation extraction