Commits

Author Commit Message Labels Comments Date
Daniel Blankenberg
Rework wiggle readers. These now return zero-based (half-open) coordinates.
Daniel Blankenberg
Update align.core.src_split() to split species, chrom from the left.
Bob Harris
changed assertion so that, on failure, the mismatched alignment blocks are shown
Daniel Blankenberg
Fix iterator when using fixedStep in wiggle.Reader().
Daniel Blankenberg
Fix for table reader returning comments for blank lines when return_comments is False.
James Taylor
Changed default for mincols from 10 to 0
James Taylor
Fix for maf_extract_ranged_indexed.py (and a test!)
Daniel Blankenberg
Fix for retrieving lists of blocks from indexes.
Daniel Blankenberg
Fix memory issues when dealing with alignments.
David King
Skip comment lines
Greg Von Kuster
Reverted Radhesh's changes that broke the cluster tool.
Bob Harris
improved failure report (MaxtriesException); got rid of tab characters
Daniel Blankenberg
Better (hopefully) fix for remove_all_gap_columns() where component.text is not of type sequence.
Daniel Blankenberg
Fix for remove_all_gap_columns() when the one of the component's sequence is not the proper
Bob Harris
added check for blank header(s) in lav h-stanza
Daniel Blankenberg
GenomicIntervalReader will now treat lines that start with "track " as comments.
radhesh
fixed segfault occurring due to infinite recursion , gops_cluster. Added some pointer checks to avoid segfaults.
Bob Harris
fixed problem when overlap is allowed; also simplified the caller's burden for generating genomic intervals
Bob Harris
updated, to reflect apparent change in file format at UCSC
Bob Harris
corrected typo
Bob Harris
separated read_lengths_file into its own module
Bob 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
_actually_ faster binary search version (rev 390 was in fact slower than rev 389)
Bob Harris
changed score to number (instead of string)
Bob Harris
allegedly faster rewrite that uses binary search
Bob Harris
(will shortly rewrite this) correcting two off-by-one errors that introduced some minor bias that is hard to describe
chinmay
Bug fix for concat.py, the gops_concat tool should now work better.
David King
Genome-wide McDonald Kreitman script
David King
fix: pass ID after reading transfac entry
David King
added support for name field in transfac
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