Recent changes to Versions

Versions modified by Tomasz

Tomasz — Mon, 04 Apr 2016 23:01:02 -0000

--- v13
+++ v14
@@ -1,4 +1,9 @@
 ##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)###

Versions modified by Tomasz

Tomasz — Sun, 07 Feb 2016 19:15:32 -0000

--- v12
+++ v13
@@ -1,4 +1,9 @@
 ##Version History##
+
+
+###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)###

Versions modified by Tomasz

Tomasz — Tue, 04 Nov 2014 07:38:12 -0000

--- v11
+++ v12
@@ -1,4 +1,10 @@
 ##Version History##
+
+
+###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)###

Versions modified by Tomasz

Tomasz — Sun, 21 Sep 2014 06:29:28 -0000

--- v10
+++ v11
@@ -1,4 +1,11 @@
 ##Version History##
+
+###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)###

Versions modified by Tomasz

Tomasz — Sun, 27 Jul 2014 11:23:15 -0000

--- v9
+++ v10
@@ -1,4 +1,9 @@
 ##Version History##
+
+###v 0.2.1 (27 Jul 2014)###
+
+* extended option --NRef to variantdetails tool.
+

 ###v 0.2.0 (18 Jul 2014)###

Versions modified by Tomasz

Tomasz — Sat, 19 Jul 2014 05:09:56 -0000

--- v8
+++ v9
@@ -1,7 +1,8 @@
 ##Version History##

-###v 0.2.0 (Jul 2014)###
+###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.

Versions modified by Tomasz

Tomasz — Tue, 15 Jul 2014 19:57:59 -0000

--- v7
+++ v8
@@ -1,5 +1,11 @@
 ##Version History##

+###v 0.2.0 (Jul 2014)###
+
+* 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)###

Versions modified by Tomasz

Tomasz — Sun, 27 Apr 2014 13:37:00 -0000

--- v6
+++ v7
@@ -1,4 +1,18 @@
 ##Version History##
+
+
+###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)###

Versions modified by Tomasz

Tomasz — Mon, 02 Dec 2013 23:20:29 -0000

--- v5
+++ v6
@@ -1,4 +1,8 @@
 ##Version History##
+
+###v 0.1.2 (3 Dec 2013)###
+
+* bug fixes, mainly in GUI

 ###v 0.1.1 (28 Aug 2013)###

Versions modified by Tomasz

Tomasz — Tue, 27 Aug 2013 22:41:00 -0000

--- v4
+++ v5
@@ -1,20 +1,20 @@
 ##Version History##

-###v 0.1.1 (coming soon)###
+###v 0.1.1 (28 Aug 2013)###

 Changes to the core toolkit:

-* added validation stringency options. This allows (via the Picard library) to process bam files with missing or malformed read groups.
-* minor edits to vcf output files to avoid warnings when indexing with igvtools.
-* added several options to “find” and “split” tools.
+* 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 feature allowing saving changes to data files (previous version only provided file viewing)
-* added support to display files and scripts under Windows.
+* 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###