[Samtools-help] Picard release 1.41

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

Picard release 1.41
14 March 2011

- SamToFastq was NPEing if @RG.PU did not exist.  I have modified it to 
fall back to using @RG.ID if @RG.PU is null and we are doing output per 
read group.

- Add SeekableHTTPStream ctor that takes a Proxy object.

- QualityScoreDistribution.java: Converted to use arrays internally to 
reduce runtime by 30-40%.

- Adding functionality to SamToFastq to optionally trim read 1 or read 2 
and to optionally write a maximum number of bases (post-trimming) to the 
fastq file.

- Added a new utility called ReorderSam (contributed by Mark DePristo) 
which is designed to take a SAM/BAM file and switch out the sequence 
dictionary for one in a different order, and then re-order the INPUT 
file to produce a coordinate sorted OUTPUT file with respect to the new 
sequence dictionary.

- AddOrReplaceReadGroups: A new utility to add or replace the (possibly 
empty) set of read groups in an existing SAM or BAM file, contributed by 
Mark DePristo.

- Modified AbstractAlignmentMerger and SamAlignment merger to handle (a) 
multiple files of alignments and (b) separate alignments of both ends of 
a paired read.

- Significant refactoring of MergeBamAlignment.  AbstractAlignmentMerger 
and SamAlignmentMerger have been modified to use the expected 
orientations of read pairs rather than a boolean for whether the library 
is a jumping library.  They have new constructors and code that uses 
these directly will have to be modified to use them.  MergeBamAlignment 
has retained JUMP_SIZE for backwards compatiblity, but it has been 
deprecated and uses should switch to providing EXPECTED_ORIENTATIONS.

- MeanQualityByCycle.java: Reverse complement all reads with the 
negativeStrandFlag set, even if they are unmapped

- Make sure BAM index is created when indexing on the fly, even when the 
output BAM does not contain any reads.

- ValidateSamFile: Flush output stream so that message that error list 
has been truncated is emitted.

- RevertSam.java: When a read has negative strand flag set, 
reverse-complement it regardless of whether it is mapped or not, and 
clear the flag.

- CollectInsertSizeMetrics.java: Changed histogram holder from HashMap 
to EnumMap so that metrics file will output in a predictable order

- NormalizeFasta.java: Added a warning message if a sequence doesn't 
have any bases while normalizing.

-Alec