nchernia
commented
6 years ago Could you do a pull request?
On Wed, Oct 18, 2017 at 1:10 PM, carlvitzthum notifications@github.com wrote:
I'm working on developing a converter from .hic to .cool files (hic2cool) and came across a possible issue with a test file of hic version 6. The binX, binY, and counts values were not correct within the readBlock function.
The file is IMR90.hic and can be found here: https://bcm.app.box.com/v/ aidenlab/folder/11235404320.
I was able to get the correct counts (i.e. ones that matched the output of juice_tools dump) by changing the lines 323 to 325 in python/straw.py. https://github.com/theaidenlab/straw/blob/65f0e94bf7cc11cfa6a9e7ddaf5020 5591bb6069/python/straw.py#L323.
Looking closely, the binX value == nRecords for i=0 in the loop over range(nRecords), which explains the problem. I changed the range of bytes read and it seems to work:
x = struct.unpack(b'<i', uncompressedBytes[(12i+4):(12i+8)])[0] y = struct.unpack(b'<i', uncompressedBytes[(12i+8):(12i+12)])[0] c = struct.unpack(b'<f', uncompressedBytes[(12i+12):(12i+16)])[0]
Just thought I would let you know in case this is a valid issue you want to fix.
Best, Carl
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carlvitzthum
theaidenlab
I'm working on developing a converter from .hic to .cool files (hic2cool) and came across a possible issue with a test file of hic version 6. The binX, binY, and counts values were not correct within the readBlock function.
The file is IMR90.hic and can be found here: https://bcm.app.box.com/v/aidenlab/folder/11235404320.
I was able to get the correct counts (i.e. ones that matched the output of
juice_tools dump) by changing the lines 323 to 325 in python/straw.py. https://github.com/theaidenlab/straw/blob/65f0e94bf7cc11cfa6a9e7ddaf50205591bb6069/python/straw.py#L323-L325Looking closely, the binX value == nRecords for i=0 in the loop over range(nRecords), which explains the problem. I changed the range of bytes read and it seems to work:
x = struct.unpack(b'<i', uncompressedBytes[(12i+4):(12i+8)])[0] y = struct.unpack(b'<i', uncompressedBytes[(12i+8):(12i+12)])[0] c = struct.unpack(b'<f', uncompressedBytes[(12i+12):(12i+16)])[0]
Just thought I would let you know in case this is a valid issue you want to fix.
Best, Carl