Versions

Version History

v 0.2.5 (4 Mar 2016)

• fix bug that caused variant caller to crash when processing unusual cigars at the start of a chromosome

v 0.2.4 (7 Feb 2016)

• upgrade to new version of library jSeqUtils. Fixes bug in fasta file readers; now possible to read fasta files with comments in the contig header (e.g ">chr1 comment")

v 0.2.3 (4 Nov 2014)

• update in variant calls - added genotype field to allow filtering of variants supported by reads with many mismatches
• updates to GUI - better control of searching and displaying subsets of data tables

v 0.2.2 (21 Sep 2014)

• update in variant calling for indels - augmented vcf entries with depth and strand bias estimates.
• fixed a bug in variant filtering - fixed problem where infinity symbols where treated as strings rather than numbers.

v 0.2.1 (27 Jul 2014)

• extended option --NRef to variantdetails tool.

v 0.2.0 (18 Jul 2014)

• Requires java 7
• Fixed an important bug in tool variantdetails. The bug caused the program to mistakenly report zeros in multiple columns in the data table for indels.
• Added command line options to treat N bases in reads as reference bases.
• Some bug fixes in GUI.

v 0.1.3 (27 Apr 2014)

Changes to core toolkit:

• variant caller and other tools now ignore reads marked as duplicates (previously, reads had to be entirely removed prior to calling)
• error rate calculation enhanced, now possible to estimate rates on selected genomic sites.

Changes to GUI:

• bug fixes and some performance improvements
• now enables viewing/saving bam files

v 0.1.2 (3 Dec 2013)

• bug fixes, mainly in GUI

v 0.1.1 (28 Aug 2013)

Changes to the core toolkit:

• added validation stringency options - this enables (via the Picard library) processing of bam files with missing or malformed read groups
• minor edits to vcf output files to avoid warnings when indexing with igvtools, additional fields in the format column to enhance filtering capabilities
• added several options to “find” and “split” tools

Changes to the GUI:

• fixed numerous bugs
• added several features into the file manager, including renaming and copying files
• added capability to edit and save changes to data files
• added support to display files and execute scripts under Windows

v 0.1.0

First public version.