V3.1.0

[bkille]

• When filtering matches, the "score" of a match no longer takes into account the length. Previously, the score for a mapping was len*ANI, meaning that a 1000bp mapping with 100% identity would be tossed out in favor of a 1112bp mapping with 90% identity.
• Fixes a rare bug that caused a crash when the very first minmer in the index is a hit.
• Fixes bug with --kmerThreshold CLI option which ignored users' argument in favor of 1.
• Low complexity segments are tossed out before stage 1 mapping.
• Mappings use 32-bit integers to store positions now instead of 64-bit integers. If you need mashmap to work with contigs larger than 2^31, you can pass -DLARGE_CONTIG=1 to CMake when building.
• Reads shorter than the block length are now split, instead of being aligned in one piece.
• Added --targetPrefix and --targetList CLI options, which allow the users to specify subsets of the reference file to be indexed. Requires htslib!
• Added --lowerTriangular CLI option which only computes mappings between sequence i and sequence j if i > j (meant to be used when reference and query files are identical).
• Limits the size of the DP filter so that large sketch sizes don't incur a huge setup time.