cgates/pulintz: Added sam parsing to IdentifyPairs; minor cleanup
cgates/pulintz: renamed files to follow python module naming convention
pulintz: minor debug of identify_pairs.py, correcting sam output.
cgates/pulintz: added wrapper scripts and updated file naming conventions
cgates/pulintz: fix silly bugs in output file name parsing
cgates: Adjusted identify_pairs to ignore unaligned reads, filter invalid L-R orientation, and pass through filtered sam input file.
cgates: Adjusted header doc
cgates:Updated header doc in identify_pairs and renamed split_file.py to partition_file.py
cgates: Adjusted header doc
cgates: completed refactor to enable polymorphic handling of unaligned reads
pulintz: modified identify_pairs.py to export split reads as paired reads.
cgates/pulintz: added scripts to use transcriptome alignment/adjusted identify pairs to correctly annotate gap distance and set flags for better viewing in IGV
cgates/pulintz: Adjusted 01-bowtie-transcriptome to emit sam file and added cluster_gaps.py
cgates/pulintz: Adjusted 01-bowtie-transcriptome to emit sam file and added cluster_gaps.py
cgates: refactored to emit sorted bed files
cgates: renamed bed_foo to gap_foo and adjusted format of gap_file output to include gap width and read width
cgates/pulintz: added scripts to automate late stage processes
cgates: refactored cluster_gaps to use a list of Gap objects instead of strings
cgates: spiked an approach to filtering gaps which span enitre reads
cgates:Small refactors to cluster steps