update NewChromSweep signature to support fisher. May have conflicts with @nkindlon's upcoming changes. Will resolve then.

added -prec option, default 10. Updated unit tests for merge, map, jaccard. Accept stdin by default in merge.

It was correctly identifying reads whose “paired” flag was set, but then
it was incorrectly skipping over the read-pair that follows such an
incorrect read.

Also added a test for this behavior.