Version 0.3.14

• New QC.sh interface.
• output check from QC.sh
• suppresses warning of bedtools in QC.sh
• fix to exception when there is no duplicate reads
• fix to when there is no non-CG cytosine pileup counts

Version 0.3.12

• Some performance tweaks, two rounds of seeding
• bsconv allows filtering by fraction of retention
• bsconv reports a summary of retention
• allow for soft-clipping by base quality in alignment, see -z option in biscuit align
• allow for additional soft-clipping in alignment see -5 and -3 in biscuit align

Version 0.3.11

• Fix rare case where seeding skipped mapping non-unique reads because of assymmetric filtering

Version 0.3.10

• A read mapping fix avoid seed chaining interference from the two bisulfite strands. This marginally improves on mapping in C-free or G-free regions.

Version 0.3.9

• important update: default alignment strand in changed -b 0 is the default and mapping happens at both strands. -b 1 (mapping happens only at parent strand, faster) is not by default.
• added rectangle subcommand to produce epi-read format of the same chromosome start and end.

Version 0.3.8

• fix to tview hard clipping
• fix to seed merging
• mergecg takes -k to filter minimum depth
• pileup optionally filter by minimum alignment score

Version 0.3.7

• insert size estimation in PE is now bounded
• bug fix to read pairing

Version 0.3.6

This version includes two important bug fixes.

• Fix to single-end amplicon pileup.
• Fix to alignment seg fault when one mate read is mapped only to decoy sequence.

Version 0.3.5

• Added QC.sh
• Ready for bioconda upload

Version 0.3.4

• multi-sample output passed VCF validator
• change to SP-tag output in SNP
• implementation to ambiguous call redistribution
• Bug fix to VCF2bed