Picard/HTSJDK Release 1.121
September 22, 2014
Picard:
Added a static function to PedFile that allows the creation of a pedFile
object from a Map<String,Sex>.
Fixed BAMRecordCodec to recognize when qual array has been changed.
Added a SortVcfs CLP that will sort VCF files by contig and genomic
position.
Supplemental alignments are now considered when fixing mate information in
FixMateInformation and RevertOriginalBaseQualitiesAndAddMateCigar.
RevertSam: Added ability to use original qualities to detect encoding
scheme if they are being restored. Modified SANITIZE method to convert all
non-Standard quality score encoding schemes to Standard. Fixed issue with
validation stringency not being propagated.
SamAlignmentMerger: Moved the test for duplicate @PG.IDs into
AbstractAlignmentMerger to avoid opening the unmapped SAM file twice.
SamToFastq: Removed redundant IOUtil.openFileForWriting() calls for the
fastq writers.
CommandLineProgram: Bugfix - the validation stringency command line option
is now passed to the sam reader factory
HTSJDK:
Significant work was done towards making HTSJDK compatible with maven-based
repositories such as Maven Central and Sonatype.
VCFContigHeaderLine: Fixed bug in setSequenceDictionary where where the
assembly value of the updated contigs was not being set properly in the VCF
header.
Fixed a bug in VCFUtils.smartMergeHeaders related to contig ordering.
Made some useful additions to SAMTestUtil
In build.xml, changed htsjdk.version.property.xml to
htsjdk.version.properties. See https://github.com/samtools/htsjdk/issues/99
Replaced use of TestNG in SAMTestUtil.
Only return the first error when validating a SAMRecord using STRICT, for
increased performance.
Added CustomReaderFactory for plugging in external implementations of
SamReader capable of getting data from APIs such as Google Genomics.
QualityEncodingDetector: Add the option of using original quality scores
for determining the encoding scheme.
Introduced several fixes related to JDK8 in SamFileHeaderMergerTest
SamPairUtil: Added methods to help set mate cigars and mate information
given a queryname sorted iterator. This is useful when we want to fix or
update the mate information, including the mate cigar.
IOUtil: Added methods to check for readability/writability of list of files
Added copyrights to some recently added classes
IntervalList: No longer enforce by default that intervals that will be
merged have the same strand
SamReaderFactory: Exposed a way to set the default validation stringency
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