Author Commit Message Labels Comments Date
Bob Harris avatarBob Harris
improved failure report (MaxtriesException); got rid of tab characters
Daniel Blankenberg avatarDaniel Blankenberg
Better (hopefully) fix for remove_all_gap_columns() where component.text is not of type sequence.
Daniel Blankenberg avatarDaniel Blankenberg
Fix for remove_all_gap_columns() when the one of the component's sequence is not the proper
Bob Harris avatarBob Harris
added check for blank header(s) in lav h-stanza
Daniel Blankenberg avatarDaniel Blankenberg
GenomicIntervalReader will now treat lines that start with "track " as comments.
Default avatar radhesh
fixed segfault occurring due to infinite recursion , gops_cluster. Added some pointer checks to avoid segfaults.
Bob Harris avatarBob Harris
fixed problem when overlap is allowed; also simplified the caller's burden for generating genomic intervals
Bob Harris avatarBob Harris
updated, to reflect apparent change in file format at UCSC
Bob Harris avatarBob Harris
corrected typo
Bob Harris avatarBob Harris
separated read_lengths_file into its own module
Bob Harris avatarBob Harris
separating throwing from gap creation; added interface that lets caller throw intervals at regions with other info attached (primarily to allow throwing at genomic intervals)
Bob Harris avatarBob Harris
_actually_ faster binary search version (rev 390 was in fact slower than rev 389)
Bob Harris avatarBob Harris
changed score to number (instead of string)
Bob Harris avatarBob Harris
allegedly faster rewrite that uses binary search
Bob Harris avatarBob Harris
(will shortly rewrite this) correcting two off-by-one errors that introduced some minor bias that is hard to describe
Default avatar chinmay
Bug fix for concat.py, the gops_concat tool should now work better.
Default avatar David King
Genome-wide McDonald Kreitman script
Default avatar David King
fix: pass ID after reading transfac entry
Default avatar David King
added support for name field in transfac
Default avatar David King
change empty zeros (numpy) to int for counts
Default avatar David King
Remove all-gap columns after removing rows of the alignment
James Taylor avatarJames Taylor
Clean up checking for valid blocks, if there were empty components the
James Taylor avatarJames Taylor
Generated C code for twobit.
Bob Harris avatarBob Harris
make score a number only if it's a string
Bob Harris avatarBob Harris
make score a number if at all possible
Bob Harris avatarBob Harris
corrected species_to_lengths when contigs occur
Default avatar chinmay
Bug fix in concat.py
Bob Harris avatarBob Harris
lav header can contain sequence names with extra stuff like (reverse complement), truncating for the sake of maf and everything else downstream
Bob Harris avatarBob Harris
updated test to match change in lav.py
Bob Harris avatarBob Harris
changed acquisition of src (species.chrom) to check h-stanza first; this means that if the aligned sequence was fasta and had a header, we fetch src from there instead of attempting to reconstruct it from the path
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