2.0.2

This release contains numerous bugfixes and several new features.

The features are adding a new -pfc option that will preserve comments in a FASTQ input into S/BAM tags; an option to attach the alignment time for each read as a BAM tag; cleaning up printf output formats by doing things like adding commas to large numbers so they're easier for humans to read; adding some options to reduce or eliminate status printing while aligning; updating to S/BAM format 1.6 and including the SO tag in the header when appropriate; increasing both the max read length and the maximum edit distance; various changes to the default parameters; and, fixes to the quick start guide and user manual.

The bugfixes include better handling of large indels enabled by the -i switch; supporting Windows-style (CRLF) FASTA files for index build; fixes in bam output; fixing some pathological cases that caused very slow read processing (during output, of all things); fix problems in non-affine gap single end alignments; fix an _int64 overflow in the Windows fine grained timer (which only affected performance measurements, but was still annoying); and, fix a bug for reads that aligned off the beginning of a contig.