From: Alec W. <al...@br...> - 2010-06-21 15:29:55
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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 |