Added TileMetricsUtil to easily get Tile-like objects out of TileMetricsOut.bin

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1410 8bce386e-0d6e-43e0-b1ca-608082c0432d
New collection utility methods

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1411 8bce386e-0d6e-43e0-b1ca-608082c0432d
Minor refactor

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1412 8bce386e-0d6e-43e0-b1ca-608082c0432d
Improve Javadoc

org.broad.igv.tribble.readers package

TODO Should we remove the LineReader interface? Somewhat redundant with LineReader in net.sf.samtools.util

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1413 8bce386e-0d6e-43e0-b1ca-608082c0432d
Have ParsingUtils call getURLHelper, so that registerHelperClass actually does something.

Also add test for loading from FTP. Ignored for now because Tribble doesn't support this out-of-the-box

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1414 8bce386e-0d6e-43e0-b1ca-608082c0432d
Have ParsingUtils support FTP out-of-the-box

Add FTPHelper as an implementation of URLHelper, and RemoteURLHelper which delegates to HTTPHelper and FTPHelper as appropriate. ParsingUtils should now, by default, support FTP. Add additional tests to make sure of this. 

Clients can still register their own helper, improved the javadoc on registerHelperClass to make it clear what was expected.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1415 8bce386e-0d6e-43e0-b1ca-608082c0432d
Remove extraneous dependency on net.sf.picard class.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1416 8bce386e-0d6e-43e0-b1ca-608082c0432d
Restore the loss of the functionality that confirmed that sam-jdk code did not depend on picard code.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1417 8bce386e-0d6e-43e0-b1ca-608082c0432d
Replace PicardException with SamException because net.sf.samtools code cannot reference net.sf.picard code.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1418 8bce386e-0d6e-43e0-b1ca-608082c0432d
Eliminate instance of Log object because net.sf.samtools code cannot reference net.sf.picard code, and logging shouldn't be necessary because exception is being propagated.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1419 8bce386e-0d6e-43e0-b1ca-608082c0432d
Correct spelling error in error enum value, and switch error regarding adjacent CIGAR I and D to the corrected enum value.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1420 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix unit test to agree with new error enum being returned for adjacent indel in cigar.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1421 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add validation of indexing bin if present and appropriate.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1422 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.90

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1423 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix unit test to agree with new error enum being returned for adjacent indel in cigar.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1429 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix bug in new validation of indexing bin.

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

git-svn-id: svn://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: svn://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: svn://svn.code.sf.net/p/picard/code/trunk@1437 8bce386e-0d6e-43e0-b1ca-608082c0432d