fixed vcf raw counts reporting bug

Author: aseetharam

Dockerfile

@@ -44,20 +44,23 @@ COPY --from=builder /wheels /wheels
 RUN pip install --no-cache-dir /wheels/* && rm -rf /wheels
 
 # Install snpEff (optional, makes image larger)
-ARG INSTALL_SNPEFF=false
+ARG INSTALL_SNPEFF=true
 RUN if [ "$INSTALL_SNPEFF" = "true" ]; then \
     apt-get update && apt-get install -y --no-install-recommends \
     default-jre-headless \
     wget \
     unzip \
-    && wget -q https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip \
+    && wget -q https://snpeff-public.s3.amazonaws.com/versions/snpEff_latest_core.zip \
     && unzip snpEff_latest_core.zip -d /opt \
     && rm snpEff_latest_core.zip \
-    && ln -s /opt/snpEff/exec/snpEff /usr/local/bin/snpEff \
     && apt-get remove -y wget unzip \
     && apt-get autoremove -y \
     && rm -rf /var/lib/apt/lists/*; \
     fi
+ENV PATH="/opt/snpEff/exec:${PATH}"
+RUN if [ -f /opt/snpEff/exec/snpeff ]; then \
+    ln -s /opt/snpEff/exec/snpeff /opt/snpEff/exec/snpEff; \
+    fi
 
 # Create non-root user
 RUN useradd -m -s /bin/bash bsaseq

src/bsaseq/cli.py

@@ -25,7 +25,7 @@
 )
 from bsaseq.analysis.windows import calculate_windows
 from bsaseq.io.summary import AnalysisSummary, write_summary
-from bsaseq.io.vcf import get_sample_names, parse_vcf, write_candidates_vcf
+from bsaseq.io.vcf import get_sample_names, parse_vcf_to_list, write_candidates_vcf
 from bsaseq.io.writers import (
     write_annotated_candidates_tsv,
     write_candidate_genes_tsv,
@@ -360,16 +360,14 @@ def run(
 
     try:
         # Parse VCF and collect variants
-        variants = list(
-            parse_vcf(
-                vcf_path=vcf,
-                high_bulk=high_bulk,
-                low_bulk=low_bulk,
-                min_dp=min_dp,
-                max_dp=max_dp,
-                min_gq=min_gq,
-                min_qual=min_qual,
-            )
+        variants, vcf_stats = parse_vcf_to_list(
+            vcf_path=vcf,
+            high_bulk=high_bulk,
+            low_bulk=low_bulk,
+            min_dp=min_dp,
+            max_dp=max_dp,
+            min_gq=min_gq,
+            min_qual=min_qual,
         )
 
         if not variants:
@@ -619,8 +617,8 @@ def run(
             vcf_path=str(vcf),
             high_bulk_samples=high_samples,
             low_bulk_samples=low_samples,
-            total_variants=len(variants),  # We don't have pre-filter count easily
-            passing_variants=len(variants),
+            total_variants=vcf_stats.total_records,
+            passing_variants=vcf_stats.passed,
             total_windows=len(windows),
             significant_windows=significant_windows,
             candidate_regions=len(regions),

src/bsaseq/io/vcf.py

@@ -129,6 +129,7 @@ def parse_vcf(
     max_dp: int = 200,
     min_gq: int = 20,
     min_qual: float = 30.0,
+    _stats: FilterStats | None = None,
 ) -> Iterator[Variant]:
     """Parse VCF and yield Variant objects.
 
@@ -194,7 +195,7 @@ def parse_vcf(
         f"min_gq={min_gq}, min_qual={min_qual}"
     )
 
-    stats = FilterStats()
+    stats = _stats if _stats is not None else FilterStats()
 
     for record in vcf:
         stats.total_records += 1
@@ -323,8 +324,8 @@ def parse_vcf_to_list(
     max_dp: int = 200,
     min_gq: int = 20,
     min_qual: float = 30.0,
-) -> list[Variant]:
-    """Parse VCF and return list of Variant objects.
+) -> tuple[list[Variant], FilterStats]:
+    """Parse VCF and return list of Variant objects with filter statistics.
 
     Convenience wrapper around parse_vcf() that returns a list
     instead of an iterator. Use with caution for large VCF files
@@ -340,13 +341,16 @@ def parse_vcf_to_list(
         min_qual: Minimum variant QUAL score.
 
     Returns:
-        List of Variant objects passing all filters.
+        Tuple of (variants, stats) where variants is a list of Variant
+        objects passing all filters and stats is the FilterStats with
+        counts for all records including those filtered out.
 
     Raises:
         ValueError: If sample names not found in VCF.
         FileNotFoundError: If VCF file does not exist.
     """
-    return list(
+    stats = FilterStats()
+    variants = list(
         parse_vcf(
             vcf_path=vcf_path,
             high_bulk=high_bulk,
@@ -355,8 +359,10 @@ def parse_vcf_to_list(
             max_dp=max_dp,
             min_gq=min_gq,
             min_qual=min_qual,
+            _stats=stats,
         )
     )
+    return variants, stats
 
 
 def write_candidates_vcf(