PeakShapeResult has no attribute hist

[IanSudbery]

The PeakShapeResult class is defined in bamtools.peakshape thus:

PeakShapeResult = collections.namedtuple(
    "PeakShapeResult",
    "interval_width npeaks "
    "peak_center peak_width peak_height peak_relative_pos "
    "nreads "
    "median closest_half_height furthest_halfheight "
    "bins counts" )

however, in several places bam2peakshape.py refers to the .hist property of a PeakShapeResult or PeakShapeCounts object. Looking at the code, I'm getting the feeling that what is now counts was once called hist, but when it was renamed, not all instances of hist were caught.

This means that if bam2peakshape is called with the argument --use-strand the error:

AttributeError: 'PeakShapeResult' object has no attribute 'hist'

will be thrown. The correction should be simple, but this really should also be covered by a test. I would do it now, but I've got a butt load of lectures to write before next week. Maybe I'll get round it later.

[IanSudbery]

Also main of bam2peakshape.buildDensityMatricies has a logging counter called c:

cgat-apps/cgat/tools/bam2peakshape.py

Line 479 in 4ac9f37

c = E.Counter()

But if you use a control file and use --use-strand then this happens:

cgat-apps/cgat/tools/bam2peakshape.py

Lines 529 to 535 in 4ac9f37

	if strand_specific and bed.strand == "-":
	features._replace(hist=features.hist[::-1])
	if control:
	for c in control:
	c._replace(hist=c.hist[::-1])
	if shifted:
	shifted._replace(hist=shifted.hist[::-1])

Meaning that c is overwritten with a PeakShapeResult object. This means an error is raised next time the counter is updated.