Commits

Author Commit Message Labels Comments Date
James Taylor
table_filter.py: option to treat first line as header even if it does not start with "#"
Greg Von Kuster
Fix bug in binned_bitsets - now handling errors in incoming lens dictionary. Added a new subclass of NiceReaderWrapper to handle ValueError, IndexError and OverflowError exceptions thorwn when creating / using bitsets.
Greg Von Kuster
Added exception handling related to integer overflow for interval operations.
James Taylor
Bitsets now aggressively check all their arguments.
James Taylor
Make Cython optional.
James Taylor
This fixes the fasta test for me, was in an infinite loop, Bob?
James Taylor
Add a "do_mask" flag for 2bit files. This is by far the slowest part of working with these files, so if you aren't using the soft masking you can turn it off. However 'N' masking is always done, since the data is invalid without it.
James Taylor
Get script_tests working again. All tests should be passing.
James Taylor
Require Cython (Pyrex evolved) to build.
James Taylor
Fix for write_with_synteny, I think the score should always be formatted this way, has someone seen something different?
Guru Ananda
Adding a new attribute called "minend" to IntervalNode. This attribute will contain the minimum end value for a node's subtree.
David King
typo
David King
The refindex parameter may now be given a species name instead, and need not be the reference species of the MAF file.
James Taylor
NibFile now checks for negative lengths (+ tests and some doc cleanup)
Daniel Blankenberg
Rework wiggle readers. These now return zero-based (half-open) coordinates. Add tests for wiggle readers.
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. Make component.alignment a weakref and change name to component._alignment. Add __deepcopy__ methods to both component and alignment (used in fusing alignments), as weakref is not compatible with python's default behavior. Add an iterator version of index.get() for returning blocks (index offsets are still processed as an array, to allow sorting).
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 type. This fixes an issue in dealing with MAF files when parse_e_rows = True.
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.
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