Merge pull request #25 from dkj/devel

pull version info from git
Added ability to convert a specific range of Illumina cycles using first_cycle and final_cycle args.
Ability to use first_cycle and final_cycle if run_info.xml present
Merge branch 'master' into npg-devel
Untabbified
Cleaned test file a little.
Merge pull request #26 from NadeemF/devel

Processing a specific cycle range - tests pass and are structured better than before. Handling of temp file is better as well. We might think about directing temp files to /tmp in some OS-nonspecific way.

General observations:
1. Excessive use of this. with class-level variables - does not seem to exist in the core picard.
2. Tests for truth for objects do not have to be explicit (i.e. obj == null or obj != null can be written simply as obj or !obj).
3. Tests are chatty. There might be a way to make them less chatty by default.
ensure test captures failure when there's an exception, e.g. current file does not exist exception when looking for info on a second tile when TILE_COUNT=1 and FIRST_TILE is not set
stop looking for info about a second tile when TILE_COUNT=1 and FIRST_TILE is not set
refactor much of the common pattern in Illumina2bamTest
remove superfluous throws from method definitions
Merge pull request #31 from dkj/devel

Illumina2bam should work with TILE_COUNT and no FIRST_TILE -  Fixes issue #27
Initial commit
Edited comments
Add default SUBSETS argument Y,MT; edited comments and docs
Updated copyright
Do not throw exception if @SQ dictionary is empty; edited comments
Added is-default DF option to PG header entry
Initial commit of test
Added SplitBamByChromosomes to -package-commands target; creates .jar file and javadoc in ant build