[Samtools-help] Picard release 1.42

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

Picard release 1.42
29 March 2011

- SAMRecordQueryNameComparator.java: Augment comparator to test 
not-primary flag and hit-index (HI) tag value, if present. Encapsulate 
read name comparator in case it gets changed.

- Restore value of SAMFileReader.defaultValidationStringency in various 
places where it is changed, so that methods that are typically main 
programs can be called in the context of some other program, and don't 
mess up the original validation stringency.

- SeekableHTTPStream.java: Eliminate work-around for SourceForge HTTP 
problem http://sourceforge.net/apps/trac/sourceforge/ticket/18367, since 
it no longer seems to be a problem.

- Added a little progress logging to SortSam.

- Changed SortingCollection to use a TreeSet in place of a 
PriorityQueue; this results in a speed up on the order of ~20% for the 
merging phase of SortingCollection when there are large numbers of temp 
files in use.

- CommandLineProgram.java: Modified to throw the original error, even if 
there is an exception when writing out the final log lines.

- SortingCollection.java: Make SortingCollection in-memory iteration 
destructive by default in order to reduce memory footprint.  If you want 
to call iterator() on a SortingCollection more than once, call 
setDestructiveIteration(false) to ensure that this will be allowed.  For 
SortingCollections that are large enough to require spilling to disk, 
iteration is non-destructive currently.

- Changes to centralize the size of buffers use in various buffering 
file read/writing classes and default them to 128kb.

- Add option to BAM index reading code to disable memory mapping of 
index file.  Memory-mapping can be problematic in Java because there is 
no way to force the release of a memory map before the garbage collector 
decides to do so, and therefore if many indices are opened and then 
closed, the JVM can run out of space in which to memory map.  By calling 
SAMFileReader.enableIndexMemoryMapping(false), RandomAccessFile is used 
rather than memory mapping, which results in slower performance but 
timely release of resources.  Change courtesy of Bob Handsaker.

-Alec