Support opening .hic files with only 1 bin per chromosome #180
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This overflow occurs when trying to estimate the block cache size of .hic files using chromosomes that are smaller than the file resolution. The overflow is caused by the implicit (and incorrect!) assumption that there are always at least two relative bin IDs mapping to each chromosome, and that is thus always safe to decrement the last chromosome bin ID by 1.
Fix a bug that could occur when converting .mcool with small genomes and coarse resolutions to .hic. When the resolution is sufficiently low, the bin table for small genomes will consist of one bin per chromosome. When creating .cool files, cooler flags the bin table for such files as tables with variable bin size. This is achieved by setting bin_size to NULL in the HDF5 file. hictk represents resolutions with integers, and cannot thus represent null values. Instead, when opening a .cool file with a table with variable bins, hictk returns 0 as file resolution. .hic files with BP unit do not support tables of variable bin sizes, thus we have to treat bin tables described above as fixed bin tables (i.e. tables with a resolution other than 0). This commit implements a workaround to for the above issue.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #180 +/- ##
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Coverage 84.91% 84.91%
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Files 119 119
Lines 10076 10079 +3
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+ Hits 8556 8559 +3
Misses 1520 1520 ☔ View full report in Codecov by Sentry. |
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Fix integer overflow in .hic cache estimation
Fixes #178
This overflow occurs when trying to estimate the block cache size of .hic files using chromosomes that are smaller than the file resolution.
The overflow is caused by the implicit (and incorrect!) assumption that there are always at least two relative bin IDs mapping to each chromosome, and that is thus always safe to decrement the last chromosome bin ID by 1.