Fix bug in new validation of indexing bin.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1433 8bce386e-0d6e-43e0-b1ca-608082c0432d
Have HttpUtils and HTTPHelper set URLConnection.setDefaultUseCaches(false)

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1434 8bce386e-0d6e-43e0-b1ca-608082c0432d
Metrics definition elaboration

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1435 8bce386e-0d6e-43e0-b1ca-608082c0432d
Introduced new options on IlluminaBasecallsToSam and IlluminaBasecallsToFastq to optionally disable Illumina-style EAMSS filtering.


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1436 8bce386e-0d6e-43e0-b1ca-608082c0432d
add a couple of tests for the min quality & max mismatches

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1437 8bce386e-0d6e-43e0-b1ca-608082c0432d
these files weren't in VCS


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1438 8bce386e-0d6e-43e0-b1ca-608082c0432d
PIC-542 disallow 0-length CIGAR element.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1439 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix CIGAR generation so there is not a 0-length element.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1440 8bce386e-0d6e-43e0-b1ca-608082c0432d
Comment out PIC-542 (don't allow 0-length CIGAR elements) until further testing can be done.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1441 8bce386e-0d6e-43e0-b1ca-608082c0432d
Re-integrated cigar validation restriction on 0-length operands

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1442 8bce386e-0d6e-43e0-b1ca-608082c0432d
Don't assert that basecalls directory is writable, just output directory, which may or may not be the same.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1443 8bce386e-0d6e-43e0-b1ca-608082c0432d
Allow for interleaved fastq files

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1444 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'