- concatenate-alignments mode: add ability to restrict output to a genomic slice (see -s and -e options).
 - API change: AlignmentSliceHelper makes it easier to parse and process genomic slices for sets of alignments.
  - concatenate-alignments mode: now transfers read groups to output in the same way that non-sorted concat does.
compact-to-sam mode: fixed writting of read groups, which were not correctly written for platform, platform unit, and library.
concatenate-alignments mode: Add a mechanism to override/define read groups/read origin info on the fly when reading alignments that did not include them. Coupled with changes to compact-to-sam, this makes it possible  to get BAM files with read groups directly from Goby alignments.
concatenate-alignments mode: Add a mechanism to override/define read groups/read origin info on the fly when reading alignments that did not include them. Coupled with changes to compact-to-sam, this makes it possible  to get BAM files with read groups directly from Goby alignments.
Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices
Improvements to goby shell script: remove quotes from variable when setting RJAVA_HOME and better code to find goby jar file (Thanks Manuele Simi for the WORKING_DIR solution).
Add random guards to QualityScoreFilter. Random guards prevent discarding all bases for a genotype if this genotype represents a major fraction of bases observed at a site. This avoids false negatives where genotypes could be discarded because quality was too low for all supporting bases, even though most bases had the same genotype. Behavior compatible with Goby 2.2.1- can be restored with a dynamic option, see option NoRandomGuard in QualityScoreFilter.
Fix possible out of ArrayIndexOutOfBoundsException.
Fix possible out of ArrayIndexOutOfBoundsException.
Fix NPE when a genomic slice is not provided.
Avoid possible java.lang.NegativeArraySizeException, when a meta comment does not include an equal sign (## muTector v1.0.47986)
Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices
Add Mutect format test. No dash required.
Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices
suggest-position-slices: Add --restrict-per-chromosome option.  When this switch is provided, slices will be restricted to start and end on the same chromosome. This is useful to produce intervals to give Mutect, for instance.
Add field to store chromosome index.
Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices
Update version numbers for 2.3 SNAPSHOT.
Fix artifact id.
Try to avoid java.lang.StringIndexOutOfBoundsException: String index out of range: 12
             	at java.lang.String.charAt(String.java:687)
             	at edu.cornell.med.icb.goby.alignments.ExportableAlignmentEntryData.buildFrom(ExportableAlignmentEntryData.java:582)