v0.13.0

Changes

• #394: Added option --aemb (abundance estimation for metagenomic binning),
  which makes strobealign output a table with estimated abundance values for
  each contig (instead of SAM or PAF). This was contributed by Shaojun Pan
  (@psj1997).
• #386: Parallelize indexing even more by using @alugowski’s
  poolSTL pluggable_sort.
  Indexing a human reference (measured on CHM13) now takes only ~45 s on a
  recent machine (using 8 threads).
• #376: Improve accuracy for read length 50 by optimizing the default
  indexing parameters. Paired-end accuracy increases by 0.3 percentage
  points on average. Single-end accuracy increases by 1 percentage point.
• #395: Previously, read length 75 used the same indexing parameters as length
  50, but the improved settings for length 50 are not the best for length 75.
  To avoid a decrease in accuracy, we introduced a new set of pre-defined
  indexing parameters for read length 75 (a new canonical read length).
• If --details is used, output X0:i SAM tag with the number of
  identically-scored best alignments
• #378: Added -C option for appending the FASTA or FASTQ comment to SAM
  output. (Idea and name of the option taken from BWA-MEM.)
• #371: Added --no-PG option for not outputting the PG SAM header
• Include ZStr in our own repository
  instead of downloading it at build time. This should make it possible to
  build strobealign without internet access.