Multi-threading

Thanks to @terhorst and the elegance of openMP, snp-dists will now use multiple threads. The default is 1 thread, but it can be set using the -j CPUS option.

You'll lava this version

• new -m "molten" output format: <id1> <id2> <dist> x N^2 for N samples
• new kseq.h
• minor Makefile changes

Publication version

• free() memory for seq/name arrays
• newest kseq.h
• add all authors
• ready for Zenodo + JOSS

Missed it by *that* much

Fix potential segfault if user provides > MAXSEQ sequences, an out-by-one error.

Thanks top @kloetzl for auditing my code so thoroughly!

For all your non-core needs

• removed stack RAM limit issue (via @kloetzl)
• ensure we don't exceeed MAX_SEQ (via @kloetzl )
• by default uppercase all letters and only compare AGTC (via @SionBayliss)
• compare all letters using -a ie. gaps and Ns
• don't auto uppercase using -k
• added TRAVIS support
• removed unused "size estimation" logic

Keep your distance

Got sick of waiting for my Perl script to finish on big alignments. This was the result. Seems 20 years later I can still code C. Even chucked in some C99 restrict goodness in the hope of SIMD compiler optimization.