For VCF and BCF writing, allow the caller to provide an IndexCreator instead of using the default.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1593 8bce386e-0d6e-43e0-b1ca-608082c0432d
Do not return non-zero exit status in SamToFastq if unmatched mates found and validation_stringency is not STRICT.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1594 8bce386e-0d6e-43e0-b1ca-608082c0432d
Do not call initialize on caller-supplied IndexCreator, but assume it has been invoked by caller.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1595 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.103

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1596 8bce386e-0d6e-43e0-b1ca-608082c0432d
Removing unneeded test output files

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1599 8bce386e-0d6e-43e0-b1ca-608082c0432d
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

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1600 8bce386e-0d6e-43e0-b1ca-608082c0432d
Have TabixReader use buffered seekable streams.

Also 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.

Add additional ISeekableStreamFactory methods. 


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1601 8bce386e-0d6e-43e0-b1ca-608082c0432d
Move appendToPath to ParsingUtils

Add isRemoteURL and isURL to HttpUtils, have it treat URLs more intelligently

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1602 8bce386e-0d6e-43e0-b1ca-608082c0432d
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