Remove quick-fingerprinting analysis (moved to bioinfo research)

[doron-st]

Remove quick-figerprinting analyssis from repo

---

Note

Medium Risk
Moderate risk because it deletes an end-to-end fingerprinting CLI/test surface and changes how bcftools mpileup region restriction is constructed (including new -R BED handling), which could alter variant-calling scope in downstream workflows.

Overview
Removes the quick-fingerprinting feature and its system test fixtures: deletes the quick_fingerprinting pipeline entrypoint, the QuickFingerprinter implementation, the example JSON config, and the associated system test/resources.

Updates hit-fraction variant calling and report dependencies: extends VariantHitFractionCaller.call_variants to accept an optional regions_bed (and treats .bed/.bed.gz passed via region as -R for backward compatibility), refactors major-alt extraction to use column apply, and switches run_no_gt_report.py to import ugbio_comparison.vcf_comparison_utils instead of comparison_utils.

^{Written by Cursor Bugbot for commit 4a25f59. This will update automatically on new commits. Configure here.}

[cursor]

Cursor Bugbot has reviewed your changes and found 2 potential issues.

Autofix Details

Bugbot Autofix prepared fixes for both issues found in the latest run.

• ✅ Fixed: Regression: call_variants now misuses previously-ignored region parameter
  • call_variants now treats BED-like region values as -R targets, preserving compatibility with callers that pass BED paths in the region argument.
• ✅ Fixed: Ground truth filtered by BED only, not intersection
  • When both region and regions_bed are set, ground-truth filtering now uses a precomputed BED intersection so denominator and called variants are restricted to the same locus set.

Or push these changes by commenting:

@cursor push 5882cc3db9

Preview (5882cc3db9)

diff --git a/ugvc/comparison/quick_fingerprinter.py b/ugvc/comparison/quick_fingerprinter.py
--- a/ugvc/comparison/quick_fingerprinter.py
+++ b/ugvc/comparison/quick_fingerprinter.py
@@ -46,8 +46,16 @@
 
     def prepare_ground_truth(self):
         ground_truths_to_check = {}
-        if self.regions_bed is None:
-            self.sp.print_and_run(f"echo {self.region} | sed 's/:/\t/' | sed 's/-/\t/' > {self.out_dir}/region.bed")
+        region_bed = f"{self.out_dir}/region.bed"
+        regions_bed_in_region = None
+        if self.region != "":
+            self.sp.print_and_run(f"echo {self.region} | sed 's/:/\t/' | sed 's/-/\t/' > {region_bed}")
+        if self.regions_bed is not None and self.region != "":
+            regions_bed_in_region = f"{self.out_dir}/regions_bed_in_region.bed"
+            self.sp.print_and_run(
+                f"bedtools intersect -a {self.regions_bed} -b {region_bed} | "
+                f"sort -k 1,1 -k 2,2n > {regions_bed_in_region}"
+            )
 
         for sample_id in self.ground_truth_vcfs:
             ground_truth_vcf = optional_cloud_sync(self.ground_truth_vcfs[sample_id], self.out_dir)
@@ -62,8 +70,9 @@
             )
             self.vpu.index_vcf(ground_truth_in_hcr)
             if self.regions_bed is not None:
+                regions_to_use = regions_bed_in_region if regions_bed_in_region is not None else self.regions_bed
                 self.sp.print_and_run(
-                    f"bcftools view {ground_truth_in_hcr} -R {self.regions_bed} -Oz -o {ground_truth_to_check_vcf}"
+                    f"bcftools view {ground_truth_in_hcr} -R {regions_to_use} -Oz -o {ground_truth_to_check_vcf}"
                 )
             else:
                 self.sp.print_and_run(
@@ -78,7 +87,7 @@
                 )
             elif self.region != "":
                 self.sp.print_and_run(
-                    f"bedtools intersect -a {hcr} -b {self.out_dir}/region.bed | "
+                    f"bedtools intersect -a {hcr} -b {region_bed} | "
                     f"sort -k 1,1 -k 2,2n > {hcr_in_region}"
                 )
             else:

diff --git a/ugvc/comparison/variant_hit_fraction_caller.py b/ugvc/comparison/variant_hit_fraction_caller.py
--- a/ugvc/comparison/variant_hit_fraction_caller.py
+++ b/ugvc/comparison/variant_hit_fraction_caller.py
@@ -21,7 +21,13 @@
         self.region = region
 
     def call_variants(self, cram: str, output_vcf: str, region: str, min_af: float, regions_bed: str | None = None) -> None:
-        regions_arg = f"-R {regions_bed}" if regions_bed is not None else (f"-r {region}" if region else "")
+        if regions_bed is not None:
+            regions_arg = f"-R {regions_bed}"
+        elif region and (region.endswith(".bed") or region.endswith(".bed.gz")):
+            # Backward compatibility: some callers pass a BED path in `region`.
+            regions_arg = f"-R {region}"
+        else:
+            regions_arg = f"-r {region}" if region else ""
         self.sp.print_and_run(
             f"bcftools mpileup {cram} -f {self.ref} -a ad,format/dp --skip-indels -d 500 {regions_arg} "
             + f"| bcftools view -i 'AD[0:1] / format/DP >= {min_af}' -Oz -o {output_vcf}"

_{This Bugbot Autofix run was free. To enable autofix for future PRs, go to the Cursor dashboard.}

[doron-st]

@cursor push 5882cc3

[cursor]

Cursor Bugbot has reviewed your changes and found 2 potential issues.

^{Bugbot Autofix is OFF. To automatically fix reported issues with cloud agents, enable autofix in the Cursor dashboard.}

[cursor]

HCR intersected with full bed, not region-restricted bed

Low Severity

When both regions_bed and region_str are provided, the ground truth VCF is correctly filtered using regions_bed_in_region (the intersection of regions_bed with the region), but the HCR bed is intersected with the full self.regions_bed instead of self.regions_bed_in_region. This inconsistency means hcr_in_region may contain regions outside the specified region_str, producing an overly broad output file.