0.6.8-pre3

This is a pre-release of sambamba, please test.

ChangeLog v0.6.8-pre3 (20180910)

Pre-release with a much faster statically compiled binary. 10-20%
faster than v0.6.6, due to ldc and LLVM improvements. Fixes speed
regression of v0.6.7 for large files due to singleobj compilation. See
also #345 and
performance

64-bit compilation should be fine on ldc 1.10. i386 target is still a problem.

• Fix mark duplicates in files with many contigs, see #361 (thanks Devon Ryan @dpryan79)
• Fix Bcftools version checking #352 (thanks Nathan S. Watson-Haigh @nathanhaigh)
• Fixate version info in BAM output headers for reproducibility. See #357
• Fixed Makefile for general use, see #332
• Started benchmarking, see #283 and https://github.com/biod/sambamba/blob/master/test/benchmark/stats.org
• Readded Travis-ci support for Linux (MacOS is disabled #338)
• Updated BioD to latest biod/BioD@5e56b2b
• Bug fixes:
  • #328 Debug version: SAM output of CRAM file is populated with debug on pipe
  • #331 Segmentation fault attempting to view header in json format
  • #335 Intel Xeon bug may segfault Sambamba - this was tracked down to an Intel Xeon bug
  • #345 sambamba index 0.6.7 takes 4x longer than 0.6.6 on the same files
• Documentation updates
• Updated lz4 to latest