[Samtools-announce] Picard release 1.23

[Alec W. <al...@br...>]

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