[Samtools-help] Picard release 1.121

[Bradley T. <br...@br...>]

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