both files: switch to using awk instead of cut to avoid delimiter problems; add --ec to bedmap call in run_10kb_counts, and add -w flag to grep statement
reflect changes to run_10kb_counts and run_generate_random_lib
change name from hotspot5 to hotspot
replace cut with awk to avert some "wavelet xfm exceeds samples size" errors
Changes to extend error-detecting and make error-handling more graceful.
Remove use of /tmp as temporary directory; all scripts now write temp files to output directories.
Remove support for jarch in run_add_peaks_per_hotspot.