Python: when c2 <= c1 output is not flipped back

[lldelisle]

Describe the bug
When fetching the contacts between 'chr1' 'chrM', it gives the same result as 'chrM' 'chr1' without any notice to the user.

To Reproduce

import numpy as np
import hicstraw
hic_file =  'ENCFF080DPJ.hic'
chrom1 = 'chr1'
chrom2 = 'chr2'
result = hicstraw.straw('observed', 'NONE', hic_file, chrom1, chrom2, 'BP', 1000000)
for i in range(10):
     print("{0}\t{1}\t{2}".format(result[i].binX, result[i].binY, result[i].counts))
result = hicstraw.straw('observed', 'NONE', hic_file, chrom2, chrom1, 'BP', 1000000)
for i in range(10):
     print("{0}\t{1}\t{2}".format(result[i].binX, result[i].binY, result[i].counts))

Expected behavior
I would expect to have the same result but with column 1 and 2 shifted.
I got exactly the same result.

The problem is that the chromosomes are flipped here:

straw/pybind11_python/src/straw.cpp

Lines 1222 to 1227 in 2525edc

	} else { // flip
	this->c1 = c02;
	this->c2 = c01;
	this->numBins1 = static_cast<int32_t>(chrom2.length / resolution);
	this->numBins2 = static_cast<int32_t>(chrom1.length / resolution);
	}

but this is information is not stored.
Therefore, the results are not flipped back in:

straw/pybind11_python/src/straw.cpp

Lines 1368 to 1374 in 2525edc

	if (!isnan(c) && !isinf(c)){
	contactRecord record = contactRecord();
	record.binX = static_cast<int32_t>(x);
	record.binY = static_cast<int32_t>(y);
	record.counts = c;
	records.push_back(record);
	}

and the matrix is not transposed in:

straw/pybind11_python/src/straw.cpp

Line 1430 in 2525edc

return py::array(py::cast(finalMatrix));

[fredlas]

Bump. This is really nasty behavior that is guaranteed to lead to miserably confusing bug hunting for anyone unlucky enough to be handed non-"canonical" data to be fed into straw. Just throw an exception if the ordering is that important.