bamliquidator_regions.m.cpp has some kind of memory error, which I'm checking in so I can continue to reproduce it and find the problem:

jd-mba:bamliquidator_internal jdimatteo$ make && ./bamliquidator_regions HG19_SUM159_BRD4_-0_+0.gff ../../copied_from_tod/05012013_C22WBACXX_3.AGTTCC.hg18.bwt.sorted.bam regions.h5
make: Nothing to be done for `all'.
about to liquidate 0: chr3 merged_SUM159_BRD4_1 90392360 -> 90502129 .
about to throw...
Skipping region 1 (chr3 merged_SUM159_BRD4_1 90392360 -> 90502129 .) due to error: liquidate failed to provide exactly one count (count is
bamliquidator_regions(15182) malloc: *** error for object 0x7fd3c200a3fc: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6
jd-mba:bamliquidator_internal jdimatteo$
regions now writes to hdf5 and opens bam file once instead of inside loop

testing with this right now:

cp region_counts.empty.h5 region_counts.h5 && make && time ./bamliquidator_regions HG19_SUM159_BRD4_-0_+0.gff ../../copied_from_tod/05012013_C22WBACXX_3.AGTTCC.hg18.bwt.sorted.bam region_counts.h5; h5diff -c region_counts.baseline.h5 region_counts.h5; echo $?
started implementing with tbb, but not thread safe yet