Folks,
I was writing a samtools/mpileup wrapper for our local use. When I delved into
how the existing samtools/sam_pileup.py adaptor worked, if found that it has a
local copy of the routine to look up the samtools .fai file in
sam_fa_indices.loc for installed genomes. I then noticed that this
Curtis,
[curtish@cheaha galaxy]$ find . -name *.py | xargs grep sam_fa_indices.loc
./tools/samtools/sam_pileup.py:seqFile = '%s/sam_fa_indices.loc' %
GALAXY_DATA_INDEX_DIR
...
./tools/ngs_rna/cufflinks_wrapper_without_gtf.py:
cached_seqs_pointer_file = os.path.join(
