fix: Convert chromsizes to int64 in cooler tiles to prevent overflow … (#157)

* fix: Convert chromsizes to int64 in cooler tiles to prevent overflow error

* Updated the readme

* Remove python3.8 tests

* Fix linter error

Author: pkerpedjiev

.github/workflows/ci.yml

@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10']
 
     steps:
     - uses: actions/checkout@v3

CHANGELOG.md

@@ -1,3 +1,7 @@
+v0.20.2
+
+- Convert cooler chromsizes to int64 to prevent overflow error with recent versions of h5py and numpy
+
 v0.20.1
 
 - Remove use of deprecated `max_chunk` argument from cooler tile fetcher.

clodius/tiles/cooler.py

@@ -57,7 +57,7 @@ def get_chromosome_names_cumul_lengths(c):
     (names, sizes, lengths) -> (list(string), dict, np.array(int))
     """
     chrom_names = c.chromnames
-    chrom_sizes = dict(c.chromsizes)
+    chrom_sizes = dict(c.chromsizes.astype(np.int64))
     chrom_cum_lengths = np.r_[0, np.cumsum(c.chromsizes.values)]
     return chrom_names, chrom_sizes, chrom_cum_lengths
 

clodius/tiles/multivec.py

@@ -261,7 +261,7 @@ def tileset_info(filename):
     if "row_infos" in f["resolutions"][str(resolutions[0])].attrs:
         row_infos = f["resolutions"][str(resolutions[0])].attrs["row_infos"]
 
-        if type(row_infos[0]) == str:
+        if isinstance(row_infos[0], str):
             try:
                 tileset_info["row_infos"] = [json.loads(r) for r in row_infos]
             except json.JSONDecodeError: