PIC-188 I hoped to use this to solve the out-of-file-handles problem, but the file handles don't appear to get released in timely fashion, so I'm just checking this in because it could be handy in the future.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@123 8bce386e-0d6e-43e0-b1ca-608082c0432d
setReadString should call setReadBases rather than setting the member directly, so BAMRecord.setReadBases gets called.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@124 8bce386e-0d6e-43e0-b1ca-608082c0432d
PIC-255 Add queryAlignmentStart() and queryMate()

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@125 8bce386e-0d6e-43e0-b1ca-608082c0432d
PIC-255 Add queryAlignmentStart() and queryMate()

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@126 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added some io asserts up front.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@127 8bce386e-0d6e-43e0-b1ca-608082c0432d
JIRA PIC-156: Performance increase by making baseBuffer an instance member

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@128 8bce386e-0d6e-43e0-b1ca-608082c0432d
PIC-256 accept zero-length bases for colorspace read

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@129 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added new short name definition for MINIMUM_MAPPING_QUALITY

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@130 8bce386e-0d6e-43e0-b1ca-608082c0432d
Changes to how reference names are interned().

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@131 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added trim() method

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@132 8bce386e-0d6e-43e0-b1ca-608082c0432d
Pushing version # for binary release 1.05

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@133 8bce386e-0d6e-43e0-b1ca-608082c0432d
added a setSequenceName()

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@136 8bce386e-0d6e-43e0-b1ca-608082c0432d
added a setSequenceName()

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@137 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add ability to read BAM file over HTTP

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@138 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add option to specify read group ID

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@139 8bce386e-0d6e-43e0-b1ca-608082c0432d
Clean up exception inheritance.  Add SAMException.  All exceptions in samtools extend that.  No PicardExceptions in samtools.  PicardException extends SAMException.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@140 8bce386e-0d6e-43e0-b1ca-608082c0432d
Increment jar version #

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@141 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add SAMFileHeader.clone()

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@144 8bce386e-0d6e-43e0-b1ca-608082c0432d
PIC-261 MarkDuplicates should write coordinate-sorted file even if input is not marked as coordinate sorted but ASSUME_SORTED=true

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@145 8bce386e-0d6e-43e0-b1ca-608082c0432d
PIC-252 Don't validate NM tag if CIGAR string is invalid, because NM tag validation requires valid CIGAR.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@146 8bce386e-0d6e-43e0-b1ca-608082c0432d