v2.5.4

bowtie2

• Added --sam-opt-config command line option for toggling SAM Opt flags.
  See MANUAL for details.
• Fixed an issue causing bowtie2's memory usage to increase over time
  when aligning BAM files.
• Changed bowtie2 to continue flushing output in the event of a partial write.
• Changed the behavior of bowtie2-build to throw an exception if it is unable
  to write the BWT (.1.bt2, .1.rev.bt2). In prior versions bowtie2-build, would silently
  ignore the error which has led some to report the absence of the BWT files in
  a "completed" index build.
• Reverted the changes made in v2.5.0 that sometimes caused unique concordant alignments to be over-counted.