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From: Alec W. <al...@br...> - 2010-06-21 19:57:38
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Hi Folks, Please note that the BAM index-writing code in this release is beta-level. The API may change and it is not ready for general use. -Alec Alec Wysoker wrote: > Picard Release 1.23 > 21 June 2010 > > - Published the following tools to the public Picard repository that > were previously maintained by Broad developers internally: > > - BamToBfq - Create one or more sets or BFQ files for input to MAQ > from a Sam or Bam file. > > - CollectAlignmentSummaryMetrics - Generate a set of summary > alignment related metrics about a Sam or Bam file. > > - CollectGcBiasMetrics - Compute a set of "GC bias" metrics about a > Sam or Bam file based on the relative distribution of aligned reads to > windows in the genome with differing GC content. > > - CollectInsertSizeMetrics - Generate tabular data and a plot of > insert sizes distributions for each pair orientation (FR, RF, FF+RR) > > - CalculateHsMetrics - Compute a set of metrics relevant for capture > or other genome sub-setting methods > > - MeanQualityByCycle - Compute mean quality by instrument cycle, > reported as text and plotted > > - QualityScoreDistribution - Produce a table of the quality score > distribution in a Sam or Bam file and a plot of the same > > - NormalizeFasta - Take a FASTA file and "normalize" it so that all > lines are of the same length (except the last line for each sequence) > > - FixMateInformation - Picard version of "samtools fixmate" that will > also pre-sort the file into queryname order, apply mate pair information > fixing and then optionally re-sort the file into the output order of the > user's choice > > - MergeBamAlignment - Tool to take a Sam or Bam file of unmapped > reads and merge it with a Sam or Bam file that contains alignment > information for a subset of those reads, retaining all metadata from the > unmapped file. > > - RevertSam - Tool to take a Sam or Bam file and "revert" it by > removing various "processed" information such as calibrated qualities, > duplicate marks, and alignment information > > > Plus the following miscellaneous changes... > > - Caching implementation of BAMFileIndex, and API to browse BAM index > independently of querying BAM file, in order to better divide work among > processors. > > - MarkDuplicates -- Handle case in which all reads for a library are > unmapped. Patch courtesy of Tom Mooney. > > - CigarUtil -- Fix so that if soft clipping results in a cigar with no > aligned bases that the read be converted to an unaligned read. > > - BAMFileReader -- Fix NPE when doing an index query in which there are > no overlapping reads. Change courtesy of Matt Hanna. > > - Add support for reading fasta with companion sequence dictionary and > faidx, for random access and ability to read portion of a sequence. > > - Add more info to exception when MD string does not work with CIGAR. > > - BlockCompressedInputStream -- Improve exception message (slightly) for > invalid uncompressed length. > > > -Alec > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > Samtools-devel mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-devel > |