perf: optimize isolate mapping with bam format and improved tooling

- Switch from SAM to BAM format for compressed file handling
- Update virtool/tools container from 1.0.0 to 1.1.0
- Add samtools 1.22.1 for efficient BAM processing
- Enhance isolate mapping performance through binary format usage

Author: igboyes

Dockerfile

@@ -1,9 +1,10 @@
 FROM python:3.12.3-bookworm AS deps
 WORKDIR /app
-COPY --from=ghcr.io/virtool/tools:1.0.0 /tools/bowtie2/2.5.4/bowtie* /usr/local/bin/
-COPY --from=ghcr.io/virtool/tools:1.0.0 /tools/hmmer/3.2.1 /opt/hmmer
-COPY --from=ghcr.io/virtool/tools:1.0.0 /tools/fastqc/0.11.9 /opt/fastqc
-COPY --from=ghcr.io/virtool/tools:1.0.0 /tools/pigz/2.8/pigz /usr/local/bin/
+COPY --from=ghcr.io/virtool/tools:1.1.0 /tools/bowtie2/2.5.4/bowtie* /usr/local/bin/
+COPY --from=ghcr.io/virtool/tools:1.1.0 /tools/hmmer/3.2.1 /opt/hmmer
+COPY --from=ghcr.io/virtool/tools:1.1.0 /tools/fastqc/0.11.9 /opt/fastqc
+COPY --from=ghcr.io/virtool/tools:1.1.0 /tools/pigz/2.8/pigz /usr/local/bin/
+COPY --from=ghcr.io/virtool/tools:1.1.0 /tools/samtools/1.22.1/bin/samtools /usr/local/bin/
 RUN apt-get update && \
     apt-get install -y --no-install-recommends default-jre && \
     rm -rf /var/lib/apt/lists/* && \

fixtures.py

@@ -37,8 +37,8 @@ def isolate_index_path(isolate_path: Path):
 
 
 @fixture
-def isolate_sam_path(isolate_path: Path):
-    return isolate_path / "to_isolates.sam"
+def isolate_bam_path(isolate_path: Path):
+    return isolate_path / "to_isolates.bam"
 
 
 @fixture

pyproject.toml

@@ -19,6 +19,7 @@ authors = [
 [dependency-groups]
 dev = [
     "maturin>=1.9.2",
+    "pysam>=0.22.0",
     "pytest>=7.4.2,<8.0.0",
     "pytest-asyncio<=0.23.8,<1.0.0",
     "pytest-mock<=3.14,<4.0.0",