Commits

History for

Commits on Jan 22, 2020

Changed method for exon edges adjustment
jmaricb
committed

Commits on Apr 2, 2019

Updated seqlib and refactored alignment
jmaricb
committed

Commits on Nov 8, 2018

Local alignment improvements
jmaricb
committed

Commits on Mar 1, 2017

Testing without conversion from unique_ptr to shared_ptr.
isovic
committed

Commits on Feb 25, 2017

Small modifications. Was testing for memory leaks, tested on an imput of 10000 same reads, and memory seems stable.
isovic
committed

Commits on Feb 23, 2017

Commits on Feb 20, 2017

Updated gindex.
isovic
committed

Commits on Feb 17, 2017

Working on Owler. This version should be functional, but it should be optimized for speed. Also, experimenting with different shapes needs to be done. One thing I learned - indexing with a minimize…
isovic
committed

Commits on Feb 16, 2017

Working on a new version of Owler.
isovic
committed

Commits on Feb 14, 2017

Changed debug output and updated gindex to better handle count cutoff.
isovic
committed

Commits on Feb 13, 2017

Changed the command line. Minimizers and thresholding are now applied by default. It can be turned off individually by tuning --minimizer-window and --threshold-hits parameters, or by using -x sens…
isovic
committed

Commits on Feb 12, 2017

Commits on Feb 11, 2017

Working on a new version of region selection which would depend on thresholding the counts, and then just compiling all hits in a single vector instead of binning. The binning process is extremely …
isovic
committed

Commits on Feb 9, 2017

Commits on Feb 4, 2017

Cleaning the IndexSpacedHashFast and debugging.
isovic
committed

Commits on Jan 22, 2017

Fixed a bug in MD generation for the first operation. Updated Edlib in seqlib to use the correct free instead of a delete. MD in semiglobal alignment was also faulty, fixed that as well.
isovic
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Commits on Jan 21, 2017

Updated Seqlib to the version with Edlib which has a bugfix for 1X instead of 1=.
isovic
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Commits on Jan 4, 2017

Fixed the second segfault in Issue #43. There were subtile index out of bounds errors due to indexing shapes (don't care position actually extend the shape beyond it's predefined number of bases). …
isovic
committed

Commits on Dec 27, 2016

Testing the transcriptome generation.
isovic
committed

Commits on Dec 19, 2016

Commits on Oct 12, 2016

Fixed Issue #32.
isovic
committed

Commits on Oct 11, 2016

Fixed Issue #34.
isovic
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Commits on Oct 7, 2016

Commits on Apr 29, 2016

Added a new parameter to skip the 'self' hits based on the sequence header name.
isovic
committed

Commits on Apr 27, 2016

Fixed Issue #21, anchorgotoh alignment should now work well. There was a problem in conversion between SeqAn alignments and the internal format. I reimplemented this function now. Also, fixed the e…
isovic
committed

Commits on Apr 22, 2016

Updated seqlib to address the gzFile_s* problem in Issue #19.
isovic
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Commits on Apr 21, 2016

Updated seqlib.
isovic
committed

Commits on Apr 14, 2016