fix a bug in ex.export_coverage.

README.md

@@ -3,7 +3,7 @@ SnapATAC2: A Python/Rust package for single-cell epigenomics analysis
 
 ![PyPI](https://img.shields.io/pypi/v/snapatac2)
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/snapatac2)
-![Continuous integration](https://github.com/kaizhang/SnapATAC2/workflows/Continuous%20integration/badge.svg)
+![Continuous integration](https://github.com/kaizhang/SnapATAC2/workflows/test-python-package/badge.svg)
 ![GitHub Repo stars](https://img.shields.io/github/stars/kaizhang/SnapATAC2?style=social)
 
 SnapATAC2 is a flexible, versatile, and scalable single-cell omics analysis framework, featuring:

docs/changelog.md

@@ -7,6 +7,10 @@
 - Add `count_frag_as_reads` argument to `pp.make_tile_matrix`, `pp.make_peak_matrix`,
   and `pp.make_gene_matrix`.
 
+### Bugs fixed:
+
+- Fix: `ex.export_coverage` generates empty files in v2.5.2.
+
 ## Release 2.5.2 (released Jan 4, 2024)
 
 ### Features:

snapatac2-core/src/export.rs

@@ -248,7 +248,7 @@ where
     fragments.for_each(|frag| {
         let not_in_blacklist = blacklist_regions.map_or(true, |bl| !bl.is_overlapped(&frag));
         let is_single = frag.strand().is_some();
-        if not_in_blacklist && is_single {
+        if not_in_blacklist {
             if ignore_for_norm.map_or(true, |x| !x.contains(frag.chrom())) {
                 total_count += 1.0;
             }

snapatac2-python/snapatac2/export/__init__.py

@@ -203,18 +203,4 @@ def export_coverage(
         adata, list(groupby), bin_size, out_dir, prefix, suffix, output_format, selections,
         blacklist, normalization, ignore_for_norm, min_frag_length,
         max_frag_length, compression, compression_level, tempdir, n_jobs,
-    )
-
-def export_bigwig(
-    adata: internal.AnnData | internal.AnnDataSet,
-    groupby: str | list[str],
-    selections: list[str] | None = None,
-    resolution: int = 1,
-    out_dir: Path = "./",
-    prefix: str = "",
-    suffix: str = ".bw",
-) -> dict[str, str]:
-    import warnings
-    warnings.warn("Use `ex.export_coverage` instead.", DeprecationWarning)
-    return export_coverage(adata, groupby=groupby, selections=selections, resolution=resolution,
-        out_dir=out_dir, prefix=prefix, suffix=suffix, output_format="bigwig")
+    )

snapatac2-python/tests/test_pipeline.py

@@ -45,7 +45,7 @@ def pipeline(data):
 
     snap.pp.make_gene_matrix(data, gene_anno=snap.genome.hg38)
 
-    snap.ex.export_fragments(data, groupby="leiden")
+    snap.ex.export_coverage(data, groupby="leiden")
 
 def test_backed(tmp_path):
     fragment_file = snap.datasets.pbmc500(downsample=True)