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.

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.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1603 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added a capacity to conditionally ignore blank lines in the fastq files. Unit tests (both positive and negative) included. Code Reivewed by Jeff.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1604 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix error in java property name.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1605 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added a capacity to conditionally ignore blank lines in the fastq files. Unit tests (both positive and negative) included. Code Reivewed by Jeff.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1606 8bce386e-0d6e-43e0-b1ca-608082c0432d
somehow the files for my tests were missing...here they are.


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1607 8bce386e-0d6e-43e0-b1ca-608082c0432d
added back a file that got deleted...oops


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1608 8bce386e-0d6e-43e0-b1ca-608082c0432d
ah! sorry. one more fix.


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1609 8bce386e-0d6e-43e0-b1ca-608082c0432d
somehow two of my directories got screwed up...fixing

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1610 8bce386e-0d6e-43e0-b1ca-608082c0432d
somehow two of my directories got screwed up...fixing

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1611 8bce386e-0d6e-43e0-b1ca-608082c0432d
Use size command in FTPUtils.getContentLength

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1612 8bce386e-0d6e-43e0-b1ca-608082c0432d
Setting the output read structure properly on IlluminaBasecallsToFastq

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1613 8bce386e-0d6e-43e0-b1ca-608082c0432d
Various updates to support internal work.

- Added alternate allele calculation method to `VariantContextUtils`.
- Made `JexlEngine` instance in `VariantContextUtils` lazy-loading to avoid classloading issues in some cases.
- Added `LogMath` utility to simplify working with values in log space.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1614 8bce386e-0d6e-43e0-b1ca-608082c0432d
Improved assertion error messages in `SAMSequenceDictionary#assertSameDictionary(SAMSequenceDictionary)`.

- Added `toString()` implementation to `SAMSequenceRecord`.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1615 8bce386e-0d6e-43e0-b1ca-608082c0432d
Handling missing read groups when requesting accumulation at level that requires read group.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1616 8bce386e-0d6e-43e0-b1ca-608082c0432d
Bug fix: Multi-threading issue in ExtractIlluminaBarcodes caused some metrics to accumulate incorrectly.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1617 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.104

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1618 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix determination of previous release ID

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1622 8bce386e-0d6e-43e0-b1ca-608082c0432d
Don't try to plot when we're not supposed to (caused by incorrectly applying a fix first used in a similar script, insertSizeHistograms.R)

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1625 8bce386e-0d6e-43e0-b1ca-608082c0432d
Reverse order of two conditions in order to avoid calling File.getUsableSpace for the last temp directory in the list.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1628 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added a method to create sequences of doubles.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1629 8bce386e-0d6e-43e0-b1ca-608082c0432d