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file_map.jsp.txt
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file_map.jsp.txt
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BLibDefinitions.h -- contains BFAST constants
Project 1 -- context sensitive gap penalty function. Completed.
Files that may need to be modified for context sensitive gap open penalty
AlignNTSpace -- does the actual alignments and calls functions in ScoringMatrix
ScoringMatrix -- defines the gap penalty functions.
AlignMatrix.c, AlignMatrix.h
ALign.c
Other files that may need to be modified to postprocess the context sensitive gap penalty.
RunLocalAlign.c print out the scoring function
RunPostProcess.c print out the scoring function Change the score comparison to a double.
AlignedReadConvert.c This file converts aligned reads into the SAM file format. This file can be modified to print out the score.
AlignedEntry.c changed the score field from int32_t to double
Project 2 -- gapped index creation. Incomplete. Tests determined it was not worthwhile.
Feb 18, 2017 -- Tested the gapped index creation. It appeared to create without any problems. Tested the matching functionality, but this caused a segmentation fault (core dump), and running process, so I don't think it is implemented.
RGIndex.c -- modified for gapped indexes. Constructs the index.
RGIndexLayout.c -- defines the index mask
Files for matching functionality.
BfastMatch -- the entry and interface to the matching program
RunMatch -- runs the matching program
RGReads.c -- This looks like the file that calls the function that does all of the work in finding the matches: RGReadsFindMatches
RGIndex.c -- RGIndexGetRangesBothStrands -> RGIndexGetRanges -> RGIndexGetIndex -> RGIndexGetHashIndexFromRead, RGIndexCompareRead
Blib.c -- WillGenerateValidKey may need to modify. Called by RGIndexGetRanges.