Better message when SortingCollection fills up TMP_DIR.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1382 8bce386e-0d6e-43e0-b1ca-608082c0432d
Change URL printed on error to point to new Getting Help section on project web.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1383 8bce386e-0d6e-43e0-b1ca-608082c0432d
Metrics updates

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1384 8bce386e-0d6e-43e0-b1ca-608082c0432d
New program IlluminaBasecallsToFastq, which will generate either multiple sets of FASTQs demultiplexed by barcode, or single set of FASTQs for all barcodes in input.
 IlluminaBasecallsToSam refactored to support reuse of multithreading implementation in IlluminaBasecallsToFastq.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1385 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix incorrectly named DataProvider.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1386 8bce386e-0d6e-43e0-b1ca-608082c0432d
Adjust maxRecordsInRam passed to ClusterConverter so that command-line option retains approximately the same behavior as before.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1387 8bce386e-0d6e-43e0-b1ca-608082c0432d
ignore intellij atlassian plug-in config file

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1388 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix build breakage due to overzealous automatic refactoring.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1389 8bce386e-0d6e-43e0-b1ca-608082c0432d
Increase Xmx for running test suite -- org.broad.tribble.readers.ReaderTest.testMassiveLines got an OOM

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1390 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix long-standing bug in SamLocusIterator in which every other locus was being skipped when emitUncoveredLoci==true and not using an interval list file.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1391 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.88

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1392 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge changes for version 1.88