Picard Release 1.14
16 Feb 2010
- In FormatUtil, set strings used to represent NaN and infinity so they
are consistent across OSs.
- Make FastaSequenceFile public, for users who want to open fasta files
with non-standard extension.
- Remove whitespace at end of lines when reading sequence from fasta.
- Java port of simple UCSC liftOver.
- Add mechanism for diagnosing failed liftover.
- Added support for bisulfite-treated reads in mismatch counting.
- Adjacent insertion & deletion in CIGAR is now acceptable. Adjacent
insertions or deletions are still errors.
- All CommandLinePrograms now print more info on what options were used
to run them. Specifically, they print all options exlicitly set on the
command line or in an OPTIONS_FILE, then a space, and then all non-null
- Now, for program and group ids, only the ones that collide get
remapped. All others are left as is.
- Add CleanSam, which soft-clips reads that hang off end of reference.
- Fix problem with sequence dictionary merging in which sequences in
different orders in multiple input SDs were not detected.
- Implemented tracking of how much duplication is due to optical
duplication in order to provide a better estimate of library size.
- Added MetricsFile.getNumHistograms() method
- Class Histogram: Added getModeBin() method. Refactored getMode() and
trim(..) to use it.
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