VarScan v2.4.0

20-Aug-2015

VarScan v2.4.0 is the first release to VarScan's new home at GitHub, http://dkoboldt.github.io/varscan/

VERSION 2.4.0 CHANGES
The major change to v2.4.0 is the implementation of a SmartFileReader class, which addresses a known bug
in Java runtime that could cause VarScan to hang if given an empty input file. Hat tip to Bina Technologies
for contributing this code.

Minor issues addressed in the current release include:
1.) A correction in the way normal_reads2 values are counted when the mutation allele is not observed. Prior
to this fix, a non-reference base would be counted as a variant allele even if it didn't match the actual mutation
allele called in the tumor. Now, only observations of the tumor variant allele will be counted and go into the FET.

2.) Improved parameter-handling logic for two flags (--validation and --strand-filter), which previously were
sometimes considered "turned on" if the user provided them, even if the value provided was a zero.

3.) Catching the rare ArrayIndexOutOfBoundsException errors thrown in the copynumber and trio functions when
VarScan encountered incomplete mpileup columns.

4.) Addressed a typo-bug for the tumor-purity parameter which only had an effect if the user provided percentage
values (e.g. 15) rather than fractions (e.g. 0.15).