Re: [Samtools-announce] [Samtools-devel] Picard release 1.23

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

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
>