diff --git a/macrel/data/models/AMP.onnx.gz b/macrel/data/models/AMP.onnx.gz index 89966cb..a60e440 100644 Binary files a/macrel/data/models/AMP.onnx.gz and b/macrel/data/models/AMP.onnx.gz differ diff --git a/macrel/data/models/Hemo.onnx.gz b/macrel/data/models/Hemo.onnx.gz index 91762e0..6d83b2c 100644 Binary files a/macrel/data/models/Hemo.onnx.gz and b/macrel/data/models/Hemo.onnx.gz differ diff --git a/macrel/data/scripts/count.ngl b/macrel/data/scripts/count.ngl index 29168d8..5dda18c 100644 --- a/macrel/data/scripts/count.ngl +++ b/macrel/data/scripts/count.ngl @@ -3,13 +3,14 @@ ngless "1.0" input = samfile(ARGV[1], name="MACREL") +# Keep only primary alignments filtered = select(input, keep_if=[{unique}]) +# Count features from filtered alignments counts = count(filtered, features=["seqname"], include_minus1=False, normalization={raw}, multiple={unique_only}) -counts = as_integer(round(counts)) write(counts, ofile=ARGV[2]) diff --git a/setup.py b/setup.py index f7dcd96..a7ee5b8 100644 --- a/setup.py +++ b/setup.py @@ -46,7 +46,6 @@ 'Intended Audience :: Science/Research', 'Programming Language :: Python', 'Programming Language :: Python :: 3', -'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10', 'Programming Language :: Python :: 3.11',