v1.3.7.1

Bumped release to keep track of help documentation.

Version 1.3.7.2

Created a new release to be consistent with bioconda naming requirements.

v1.3.6

Fixed missing quality string for unaligned sequences.

v1.3.5

Fix typos in help page and index step.

1.3.4

Patches whole genome alignment.

Routine maintenance

This fixes bugs including:

• Missing NM tag in SAM output.
• Incorrectly assigned mapqv with --noMismatch

1.3.2

version 1.3.2 fixed some bugs which caused aligning pass the end.

1.3.1

Removed code to find inversion between clusters in the refinement step.

Release 1.3.0

In this release, we fixed:

bug caused crash when aligning contigs.
bug related to IO when using streamed FASTQ/FASTA input.

Release 1.2.0

In this release has support for:

• Improved accuracy of indel alignments from contigs.
• Nested SV (inversion+deletion, inverted duplication).
• Improved speed for contig alignment.