Add commons-logging jar to module dependencies.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1395 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add commons-logging to MergeVcfs and SplitVcfs executable jars so that outputting BCF format works.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1396 8bce386e-0d6e-43e0-b1ca-608082c0432d
For non-demultiplex mode, don't require barcode files.

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1397 8bce386e-0d6e-43e0-b1ca-608082c0432d
Adding PCT_TARGET_BASES_40X thru _100X and HS_PENALTY_40X thru _100X metrics

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1398 8bce386e-0d6e-43e0-b1ca-608082c0432d
PCT_TARGET_BASES_100X, not PCT_TARGET_BASES_1000X

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1399 8bce386e-0d6e-43e0-b1ca-608082c0432d
VCF header lines cannot contain angle brackets in the ID field

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1400 8bce386e-0d6e-43e0-b1ca-608082c0432d
More defensive programming: don't allow bad values in VCF keys and IDs

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1401 8bce386e-0d6e-43e0-b1ca-608082c0432d
Removing pct target bases 40x..100x from TargetedPcrMetrics

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1402 8bce386e-0d6e-43e0-b1ca-608082c0432d
Remove redundant SeekableStream class

Add "readFully" method back to SeekableStream class, much in IGV depended on it.
Add registration and getting of URLHelper to ParsingUtils

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1403 8bce386e-0d6e-43e0-b1ca-608082c0432d
Improve Javadoc

Focused on bed package and examples

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1404 8bce386e-0d6e-43e0-b1ca-608082c0432d
Improve Javadoc

Update gelixtext package

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1405 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.89

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1406 8bce386e-0d6e-43e0-b1ca-608082c0432d
Improve Javadoc

Update index package mainly, also reposition/reformat many author tags

git-svn-id: svn://svn.code.sf.net/p/picard/code/trunk@1409 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge svn version 1.89