gmcvicker / genome Goto Github PK

Right now load_bam_read_depth.py will count regions between a split read as being covered by that read. A --split option could be added for RNA-seq libraries.

The implementation could be done by either using pybedtools if adding a dependency is okay, or reimplementing BedTools' strategy of looking at cigar N and D operations to compute coverage. Alternatively, pysam's pileup could be used then ignore reads at each position with the is_del flag set.

This is something I can do but which changes you'd be comfortable with, if any, is worth getting feedback on.

c/program/test_bedgraph.c is missing but is required by target program/test_bedgraph.o in program/SConscript

Hi there,

Attempting to compile this on OSX 10.8 results in the following error:

clang -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64 build/temp.macosx-10.8-intel-2.7/wig.o -lgenome -o build/lib.macosx-10.8-intel-2.7/wig.so
ld: library not found for -lgenome
clang: error: linker command failed with exit code 1 (use -v to see invocation)

typically -lXXX refers to a library to import, but there's no genome.dylib in /usr/local/lib. Nevertheless I've found that the clang bundle works just fine without -lgenome, and the installation proceeds normally thereafter. Perhaps this flag is unnecessary?