Merge pull request #64 from nkindlon/master

Fixed merge bugs w/ sort order and chrom change, added unit tests
Merge pull request #67 from nkindlon/master

Added jaccard w/ -split and unit tests. Fixed Bam input as bam output bu...
[DOC] fix formatting for unionbedg
[DOC] fix formatting for unionbedg
Merge pull request #68 from nkindlon/master

Added stranded info to jaccard and merge help, fixed stranded jaccard bu...
Merge pull request #69 from nkindlon/master

added changes to stop CLANG compiler warnings.
Update installation.rst
Merge pull request #75 from alexpenson/patch-1

Update installation.rst
Merge pull request #76 from nkindlon/master

Stripped whitespace and DOS endLine chars in parsing.
Changes fetch columns by number from BAM files.
Resolved merge conflicts with KeyListOps.cpp, test-merge.sh, and test-map.sh