Version 2.0.3

• Rewrote core sub-routine in phase 2 (quantification) for increased speed
• Fixed bug in recursive read-group analysis with file-name paths
• Fixed bug in making log file during MIRNA analysis by maple

Version 2.0.2

Modified sub-routine 'get_islands' to increase speed, especially when dealing with highly fragmented reference genomes (with lots of chromosomes / scaffolds / contigs). Thanks to Haoyu Cheng for suggesting this enhancement.

Version 2.0.1

• fixed bug that was causing option --bowtie_cores to be ignored.
• updated maple to version 0.1.1
• updated butter to version 0.2.4.1

Version 2.0.0

Major update!
Summary of major changes:

1. Method for de novo cluster discovery has changed. 'Islands' are now defined as continuous stretches of non-zero read coverage where at least one position exceeds the min_depth. This results in larger clusters relative to the previous approach.
2. Alignments are now required to be performed by the 'butter' aligner. Butter is now included in the ShortStack package.
3. MIRNA and hairpinRNA analysis is now performed by a separate program, 'maple'. Maple is now included in the ShortStack package. Use of maple with default settings cuts down dramatically on the number of non-MIRNA hairpin loci that are found.

v1.2.4.1

January 21, 2014
Same as 1.2.4, except fixed README file
Fixed several bugs that were inappropriately handling file paths that began with or contained "../"

v1.2.4

January 21, 2014
Fixed several bugs that were inappropriately handling file paths that began with or contained "../"

v1.2.3

November 1, 2013
Fixed bug where samtools was creating meaningless warning messages with some samtools versions.
Fixed bug that was not allowing appropriate exit when the bam file failed to pass validation.
Fixed bug that was causing the final cluster in a de novo run to not be reported.
Updated documentation to reflect the treatment of reference genome names with whitespaces.

v1.2.2

October 26, 2013
Fixed bug that was causing ShortStack to claim RNALfold and RNAeval weren't installed in cases where the Vienna RNA version was 1.x instead of 2.x

v1.2.1

October 23, 2013
Added support for using more than one processor core during bowtie alignment via new option --bowtie_cores
Updated documentation to reflect publication of manuscript in the journal Methods

v1.2.0

October 16, 2013.

Added support for adapter trimming and alignment of colorspace data produced by ABI SOLiD instruments via new options --untrimmedCS, --untrimmedCSQV, --trimmedCS, and --trimmedCSQV.