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)
Add some debug methods.
Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices
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)
Merge branch 'concat-slices' of bitbucket.org:fac2003/goby into concat-slices
Remove left-over filter for somatic variations.
Fix suggest-position-slices (bug would leave out some slices when restrict-with-chromosome was active).
Fix suggest-position-slices (end of chromosome too long by one base).