Homebrew/homebrew-science — pull request #561 by lparsons (2013-12-20 17:39:20+00:00)
Title: Updated picard-tools to version 1.105

Picard release 1.105
16 December 2013

- IOUtil.java: Reverse order of two conditions in order to avoid calling File.getUsableSpace for the last temp directory in the list.

- MathUtil.java: Added a method to create sequences of doubles.

Picard release 1.104
2 December 2013

- Use Intel hardware-accelerated Deflater for writing BAM files where appropriate. This is only supported on unix systems. net.sf.samtools.util.zip.IntelDeflater is used instead of java.util.zip.Deflater. See https://sourceforge.net/apps/mediawiki/picard/index.php?title=IntelDeflater

In order to use IntelDeflater, a shared library libIntelDeflater.so must be dynamically loaded. This library is included in the picard-tools zipfile. The shared library is found via one of the following methods:

If -Dsamjdk.intel_deflater_so_path is set and points to the shared library, it is loaded from that location.
Else if the shared library is in the same directory as the Picard jar that is executing, it is loaded from that location. We presume that this will be the typical way in which the shared library will be found.
Else if the shared library is found on LD_LIBRARY_PATH, it is loaded from there.
Else java.util.zip.Deflater is used.

Use of IntelDeflater may be suppressed with -Dsamjdk.try_use_intel_deflater=false.

In the header line written by Picard command-line programs, at the end of the line will appear either IntelDeflater or JdkDeflater to indicate which has been loaded.

We have seen compression time reduced by 13% to 33% depending on the hardware.

- Tribble.java: More intelligent determination of index file path; Treat URLs with query strings properly, add index extension to the path element not just the end of the string

- Have TabixReader use buffered seekable streams.

- Allow TabixReader to take an index file as an input parameter, instead of just adding an extension. This is necessary for URLs with query parameters.

- Added a capacity to conditionally ignore blank lines in the fastq files.

- Setting the output read structure properly on IlluminaBasecallsToFastq when there are
skips.

- Improved assertion error messages in `SAMSequenceDictionary#assertSameDictionary(SAMSequenceDictionary)`.

- MultiLevelCollector.java: Handling missing read groups when requesting accumulation at level that requires read group.

- Fix multi-threading bug in ExtractIlluminaBarcodes caused some metrics to accumulate incorrectly.