Merge from branch ec2
Update to properly refer to gem indices
allow stripping chromosome names when debugging read pairs
updated documentation
fix markdown
remove extra header
make summary print results to stdout
fix some bugs in import and export
whirr upgrades
merge from whirr branch
make reader just dump raw SAM records into HDFS to be sorted later
log read counts as records are read
command to sort and prep imported BAM files
attempts to optimize reading in BAM files
add option to filter out insertion calls next to bins with no coverage (good for BWA PE alignments)
change how cb home dir specified
add BWA aligner; refactor aligners
Merge branch 'import-sort-bam'
fix bwa sam read pairing
refactor and clean up some duplicated code