Use SAMFilePEHitLoader as default hitloader, resolve the issue that exact second read 5' end pos is hard to deduct from the first read
Now SEM is able to process sorted (either name or coordinate sorted) pair-end bam file without the need of filtering reads by flags
Packed based on seqcode-core commit @9f2682a4125ec08d690cf9ca123fd966bc38df1a