0.16alpha.39: fix bug that would align reads past the end of a contig, and one that would blow an assert if max insert was bigger than the padding at the beginning of the first contig
merge
0.16alpha.39: Fix RG/PG lines in header
Various minor bug fixes and perf tweaks
Merge branch 'dev' of https://github.com/amplab/snap into dev
Yet another attempt at a faster binary search that went slower, and is ifdeffed out
Change 'piece' to 'contig' so that it corresponds better to standard terminology
0.16alpha.40: Don't use secondary reads unless -sa is supplied
Try to fix Linux build
0.16alpha.41: Don't penalize as much paired-end reads that have to be aligned singly
Destroy lock in ~DecompressDataReader
Correct lock fix
0.16alpha.42 fix allocator issues on linux
Merge branch 'dev' of github.com:amplab/snap into dev
Truncate read id at space for pair matching
0.16alpha.43: support for preserving soft & hard clipping from reads that come from SAM or BAM files
Merge & fix compiler warning
Remove debugging printf
Remove extra DestroyExclusiveLock from merge
Adjust cigar strings to better match BWA/VCF conventions