8000 Commits · mttmartin/splice_detection · GitHub

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Commits

Commits on Apr 17, 2015

Initialize all values for Read class
mttmartin
committed
Fixed some warnings given by GCC's -Wall (comparing signed and unsigned ints). Also fixed undefined behavior caused by undefined finished value in ThreadPool.
mttmartin
committed

Commits on Apr 16, 2015

Fixed a problem which kept antisense reads from being considered
mttmartin
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Commits on Apr 15, 2015

Remove some code from earlier debugging
mttmartin
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Close read file upon exit.
mttmartin
committed
Added a frequency field to results. The frequency for a read is specified by an integer within parentheses in the ID of the read.
mttmartin
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Commits on Apr 14, 2015

Add log file which provides summary information
mttmartin
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Commits on Mar 19, 2015

Cleanup variable names in location_in_genome.
mttmartin
committed

Commits on Mar 18, 2015

Use seqan library for locating read parts in genome. This has significantly increased performance by about 50x. Note that the seqan library is now required to compile the program. This fixes issue #7.
mttmartin
committed

Commits on Mar 17, 2015

Created implementation of Knuth-Morris-Pratt algorithm.
mttmartin
committed

Commits on Mar 16, 2015

Make variable names in the ThreadPool more generic.
mttmartin
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Commits on Mar 15, 2015

Commits on Mar 13, 2015

Commits on Mar 12, 2015

Commits on Mar 6, 2015

Commits on Mar 2, 2015

Commits on Mar 1, 2015

Added support for antisense reads. Cleaned up debugging output related to opening FASTA files. Added optoins to paramcontainer for considering reverse and antisense reads.
mttmartin
committed

Commits on Feb 17, 2015

Added support for reversed sequences directly to program, so it is not required to run the program externally with a reversed genome sequence.
mttmartin
committed

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