feat!: only allow one BAM file + port more code to Rust

README.md

@@ -123,7 +123,7 @@ long read data should still work.
 
 ```bash
 strkit call \
-  path/to/read/file.bam \  # [REQUIRED] At least one indexed read file (BAM/CRAM)
+  path/to/read/file.bam \  # [REQUIRED] One indexed read file (BAM/CRAM)
   --hq \  # If using PacBio HiFi reads, enable this to get better genotyping & more robust expansion detection
   --realign \  # If using PacBio HiFi reads, enable this to enable local realignment / read recovery. Good for detecting expansions, but slows down calling.
   --ref path/to/reference.fa.gz \  # [REQUIRED] Indexed FASTA-formatted reference genome
@@ -146,10 +146,6 @@ If you're using HiFi reads as input, **use the `--hq` and `--realign` options**
 genotype calculation and a greater proportion of reads incorporated into the computed genotypes, 
 respectively. These should not add much performance overhead.
 
-If more than one read file is specified, the reads will be pooled. This can come in handy if you
-have e.g. multiple flow cells of the same sample split into different BAM files, or the reads are
-split by chromosome.
-
 If you want to **incorporate haplotagging from an alignment file (`HP` tags)** into the 
 process, which should speed up runtime and potentially improve calling results, you must pass 
 the `--use-hp` flag. **This flag is experimental, and has not been tested extensively.**

requirements.txt

@@ -3,33 +3,33 @@ click==8.1.7
 coverage==7.4.1
 Cython==3.0.8
 exceptiongroup==1.2.0
-Flask==3.0.2
-importlib-metadata==7.0.1
+Flask==3.0.3
+importlib_metadata==7.1.0
 iniconfig==2.0.0
-itsdangerous==2.1.2
+itsdangerous==2.2.0
 Jinja2==3.1.3
 joblib==1.3.2
 MarkupSafe==2.1.5
 numpy==1.26.4
-orjson==3.9.13
-packaging==23.2
+orjson==3.10.3
+packaging==24.0
 pandas==2.2.0
 parasail==1.3.4
 patsy==0.5.6
 pluggy==1.4.0
-pyparsing==3.1.1
-pysam==0.22.0
+pyparsing==3.1.2
+pysam==0.22.1
 pytest==7.4.4
 pytest-cov==4.1.0
 python-dateutil==2.8.2
 pytz==2024.1
-scikit-learn==1.4.0
-scipy==1.12.0
+scikit-learn==1.4.2
+scipy==1.13.0
 six==1.16.0
-statsmodels==0.14.1
-strkit_rust_ext==0.10.0
-threadpoolctl==3.2.0
+statsmodels==0.14.2
+strkit_rust_ext==0.11.0
+threadpoolctl==3.4.0
 tomli==2.0.1
 tzdata==2023.4
-Werkzeug==3.0.1
+Werkzeug==3.0.2
 zipp==3.17.0

setup.py

@@ -22,7 +22,7 @@
         "scikit-learn>=1.2.1,<1.5",
         "scipy>=1.10,<1.14",
         "statsmodels>=0.14.0,<0.15",
-        "strkit_rust_ext==0.10.0",
+        "strkit_rust_ext==0.11.0",
     ],
 
     description="A toolkit for analyzing variation in short(ish) tandem repeats.",