Author Commit Message Labels Comments Date
Guru Ananda avatarGuru Ananda
Modified intervals join function to include minimum-overlap value.
Bob Harris avatarBob Harris
fixed slicing for -strand reference again; last time I did not get it right; have also added self-test this time
Bob Harris avatarBob Harris
many fixes related to negative strand components
Bob Harris avatarBob Harris
changed error message
Guru Ananda avatarGuru Ananda
Modified BitSetSafeReaderWrapper to use chr, start, end and strand columns from the input dataset, instead of using standard values.
Bob Harris avatarBob Harris
recommitting earlier change, involving correction of how intervals are handled on negative strand
Bob Harris avatarBob Harris
backing out latest change in lieu of testing
Bob Harris avatarBob Harris
fixed problem that occurred when the reference strand was negative
Bob Harris avatarBob Harris
fixed problem that occurred when the reference strand was negative
Daniel Blankenberg avatarDaniel Blankenberg
Add an iterator to AbstractIndexedAccess and AbstractMultiIndexedAccess which returns the index and offset along with the value contained at the offset.
Nate Coraor avatarNate Coraor
Per James, make the build-time numpy dependency conditional (this is so
Daniel Blankenberg avatarDaniel Blankenberg
Remove recursive call from interval.io.BitsetSafeReaderWrapper.next().
James Taylor avatarJames Taylor
Fix for twobit on 64bit platforms (fixes ticket #7)
James Taylor avatarJames Taylor
Make labels optional in newick parser, add tests from markd (fixes ticket #3)
James Taylor avatarJames Taylor
Update pyparsing to latest version (1.5.0)
James Taylor avatarJames Taylor
Fix comparisons operations (from markd@soe.ucsc.edu, fixes ticket #4)
James Taylor avatarJames Taylor
Do not pkg_resource.require bx-python from inside bx-python
James Taylor avatarJames Taylor
Include TY (type) lines in motif parsing
James Taylor avatarJames Taylor
Fix package data (for template.ps)
James Taylor avatarJames Taylor
Support for optional short options (specifying a long option only) in
James Taylor avatarJames Taylor
Writer for transfac format, parser now handles "BS" lines as produced by
James Taylor avatarJames Taylor
Use sorted alphabet for drawing logos.
James Taylor avatarJames Taylor
Use static inline only. This gives the same effect in C89+GNU and C99, and compiles just fine on solaris with the sun pro compilers.
James Taylor avatarJames Taylor
Fixes to seqmapping and associated tests (test problems, type
James Taylor avatarJames Taylor
motif.pwm: Scoring sequences with gaps,
James Taylor avatarJames Taylor
bx.motif: Drawing sequence logos from count/frequency matrices in EPS format.
James Taylor avatarJames Taylor
bx.align.tools.thread: Need to use a deepcopy here to avoid affecting the original Alignment.
James Taylor avatarJames Taylor
motif.pwm.ScoringMatrix: unscored positions are set to nan.
James Taylor avatarJames Taylor
Transfac Reader: requiring the matrix prefixes to always start at "01" was
James Taylor avatarJames Taylor
New motif/matrix classes. Includes a reader for TRANSFAC style databases
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