History

0.1.5 (2016-01-08)

Fix bug in score_feature introduced in 0.1.2: careless use of a generator expression caused aligned_segments_in_bin to be consumed when gathering forward_aligned_segments, so reverse_aligned_segments was always empty, resulting in low cut point counts.

Change bin key construction to ensure the R script treated bins as characters.

Stop insisting motif input files match an official BED format; as long as the first six fields work, ignore the rest and get on with it.

0.1.4 (2015-12-17)

When generating an aggregate matrix, ensure that there is always a line for each position, fragment size bin, and strand, even if there is no signal there.

Support reading motifs from standard input, which required removing time estimates, and returning the motif from atactk.metrics.score_feature.

Remove option for reverse feature shift.

0.1.3 (2015-12-10)

Speed up scoring.

Open the alignment file once in each worker process, instead of in each call to score_feature. There’s a surprising amount of overhead in pysam’s opening of BAM files. The actual fetch calls are really quick.

The AlignmentFile instances are not supposed to be safe to share between processes, so each worker still has to have its own, but it’s a big reduction in overhead; things are roughly twice as fast now.

Also refactor make_cut_matrix, mainly to enable profiling.

0.1.2 (2015-12-06)

Fix an overlooked realization of the list of motifs, which would be copied into all processes. Use a generator expression for the results when using only one process.

Convert a couple of other list comprehensions to generator expressions.

Change –parallel default to 1.

Improve logging.

0.1.1 (2015-12-01)

Arbitrary cut point location.

Now you can specify where (or whether) the cut point happens relative to the ends of reads. We’re using this to compare our footprinting with DNase-seq data.

0.1.0 (2015-10-31)

• First release.