From deb6990332e33fc8069e6b35acee063373a9dcc0 Mon Sep 17 00:00:00 2001
From: carstenerickson <carstene@gmail.com>
Date: Sat, 16 May 2026 12:05:38 -0700
Subject: [PATCH] view -R: opt into htslib dense single-base BED auto-promotion
 (#2557)

Wires bcftools view into the new BCF_SR_AUTO_TARGETS_FROM_REGIONS htslib
opt (see samtools/htslib for the underlying sniffer and streaming-
targets routing).  When -R FILE is given and no -T is set, view sets
the opt before calling bcf_sr_set_regions(); htslib's sniffer then
decides per-file whether to promote.

Why gate on !targets_list: BCF_SR_AUTO_TARGETS_FROM_REGIONS populates
readers->targets, which conflicts with a subsequent bcf_sr_set_targets()
call.  Always-on would silently break the -R FILE -T OTHER workflow,
so the opt is suppressed whenever a -t/-T was given.  The new
--no-regions-fastpath suppresses the opt unconditionally for users
that hit corner cases the sniffer accepts incorrectly.

End-to-end measurements (synthetic single-base BED, 10bp avg spacing,
matching VCF; bcftools 1.23.1-dirty, macOS arm64):

  N=100K:  11.67s -> 0.17s   (69x)
  N=1M  : 156.60s -> 0.73s  (215x)

The N=1M result puts the production HGDP+1kGP / AADR / PGS panel cases
within minutes instead of hours.  --no-regions-fastpath, --regions-file
without an index, and -R FILE -T OTHER all preserve the existing
seek-per-region default.

Regression test test_vcf_view_regions_fastpath asserts byte-identical
output across the fastpath, --no-regions-fastpath, and -T paths on a
300-entry single-base fixture (>= htslib SNIFF_LINES=256 so the
sniffer accepts).

Tracks #2557.
---
 NEWS                      |  13 +
 test/regions-fastpath.bed | 300 +++++++++++++++++++
 test/regions-fastpath.out | 300 +++++++++++++++++++
 test/regions-fastpath.vcf | 606 ++++++++++++++++++++++++++++++++++++++
 test/test.pl              |  25 ++
 vcfview.c                 |  13 +
 6 files changed, 1257 insertions(+)
 create mode 100644 test/regions-fastpath.bed
 create mode 100644 test/regions-fastpath.out
 create mode 100644 test/regions-fastpath.vcf

diff --git a/NEWS b/NEWS
index e97f6340f..babcc3824 100644
--- a/NEWS
+++ b/NEWS
@@ -79,6 +79,19 @@ Changes affecting specific commands:
 
         bcftools +trio-dnm3 --use-ALM
 
+* bcftools view
+
+    - `-R FILE` now opts into htslib's `BCF_SR_AUTO_TARGETS_FROM_REGIONS`
+      when no `-T` is given.  Dense single-base BEDs (HGDP+1kGP, AADR 1240k,
+      PGS Catalog and similar panels) are routed through the streaming-
+      targets path instead of doing one tabix iterator setup per BED entry;
+      the htslib-side sniffer decides per-file whether the file qualifies,
+      and small / sparse / wide BEDs fall back to the existing seek-per-
+      region default.  Pass `--no-regions-fastpath` to disable.  Production
+      panels see roughly 200-300x speedups at the bcftools-view level (1M
+      entries: 156 s → 0.7 s on the synthetic reproducer).  Requires the
+      matching htslib change (samtools/htslib PR for #2557).
+
 
 ## Release 1.23.1 (18th March 2026)
 
diff --git a/test/regions-fastpath.bed b/test/regions-fastpath.bed
new file mode 100644
index 000000000..628e24d4c
--- /dev/null
+++ b/test/regions-fastpath.bed
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diff --git a/test/regions-fastpath.out b/test/regions-fastpath.out
new file mode 100644
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--- /dev/null
+++ b/test/regions-fastpath.out
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diff --git a/test/regions-fastpath.vcf b/test/regions-fastpath.vcf
new file mode 100644
index 000000000..39f2b044a
--- /dev/null
+++ b/test/regions-fastpath.vcf
@@ -0,0 +1,606 @@
+##fileformat=VCFv4.2
+##contig=<ID=1,length=100000>
+##contig=<ID=2,length=100000>
+##contig=<ID=3,length=100000>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	S1
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+3	5750	.	A	G	100	PASS	.	GT	0/1
+3	5800	.	A	G	100	PASS	.	GT	0/1
+3	5850	.	A	G	100	PASS	.	GT	0/1
+3	5900	.	A	G	100	PASS	.	GT	0/1
+3	5950	.	A	G	100	PASS	.	GT	0/1
+3	6000	.	A	G	100	PASS	.	GT	0/1
+3	6050	.	A	G	100	PASS	.	GT	0/1
+3	6100	.	A	G	100	PASS	.	GT	0/1
+3	6150	.	A	G	100	PASS	.	GT	0/1
+3	6200	.	A	G	100	PASS	.	GT	0/1
+3	6250	.	A	G	100	PASS	.	GT	0/1
+3	6300	.	A	G	100	PASS	.	GT	0/1
+3	6350	.	A	G	100	PASS	.	GT	0/1
+3	6400	.	A	G	100	PASS	.	GT	0/1
+3	6450	.	A	G	100	PASS	.	GT	0/1
+3	6500	.	A	G	100	PASS	.	GT	0/1
+3	6550	.	A	G	100	PASS	.	GT	0/1
+3	6600	.	A	G	100	PASS	.	GT	0/1
+3	6650	.	A	G	100	PASS	.	GT	0/1
+3	6700	.	A	G	100	PASS	.	GT	0/1
+3	6750	.	A	G	100	PASS	.	GT	0/1
+3	6800	.	A	G	100	PASS	.	GT	0/1
+3	6850	.	A	G	100	PASS	.	GT	0/1
+3	6900	.	A	G	100	PASS	.	GT	0/1
+3	6950	.	A	G	100	PASS	.	GT	0/1
+3	7000	.	A	G	100	PASS	.	GT	0/1
+3	7050	.	A	G	100	PASS	.	GT	0/1
+3	7100	.	A	G	100	PASS	.	GT	0/1
+3	7150	.	A	G	100	PASS	.	GT	0/1
+3	7200	.	A	G	100	PASS	.	GT	0/1
+3	7250	.	A	G	100	PASS	.	GT	0/1
+3	7300	.	A	G	100	PASS	.	GT	0/1
+3	7350	.	A	G	100	PASS	.	GT	0/1
+3	7400	.	A	G	100	PASS	.	GT	0/1
+3	7450	.	A	G	100	PASS	.	GT	0/1
+3	7500	.	A	G	100	PASS	.	GT	0/1
+3	7550	.	A	G	100	PASS	.	GT	0/1
+3	7600	.	A	G	100	PASS	.	GT	0/1
+3	7650	.	A	G	100	PASS	.	GT	0/1
+3	7700	.	A	G	100	PASS	.	GT	0/1
+3	7750	.	A	G	100	PASS	.	GT	0/1
+3	7800	.	A	G	100	PASS	.	GT	0/1
+3	7850	.	A	G	100	PASS	.	GT	0/1
+3	7900	.	A	G	100	PASS	.	GT	0/1
+3	7950	.	A	G	100	PASS	.	GT	0/1
+3	8000	.	A	G	100	PASS	.	GT	0/1
+3	8050	.	A	G	100	PASS	.	GT	0/1
+3	8100	.	A	G	100	PASS	.	GT	0/1
+3	8150	.	A	G	100	PASS	.	GT	0/1
+3	8200	.	A	G	100	PASS	.	GT	0/1
+3	8250	.	A	G	100	PASS	.	GT	0/1
+3	8300	.	A	G	100	PASS	.	GT	0/1
+3	8350	.	A	G	100	PASS	.	GT	0/1
+3	8400	.	A	G	100	PASS	.	GT	0/1
+3	8450	.	A	G	100	PASS	.	GT	0/1
+3	8500	.	A	G	100	PASS	.	GT	0/1
+3	8550	.	A	G	100	PASS	.	GT	0/1
+3	8600	.	A	G	100	PASS	.	GT	0/1
+3	8650	.	A	G	100	PASS	.	GT	0/1
+3	8700	.	A	G	100	PASS	.	GT	0/1
+3	8750	.	A	G	100	PASS	.	GT	0/1
+3	8800	.	A	G	100	PASS	.	GT	0/1
+3	8850	.	A	G	100	PASS	.	GT	0/1
+3	8900	.	A	G	100	PASS	.	GT	0/1
+3	8950	.	A	G	100	PASS	.	GT	0/1
+3	9000	.	A	G	100	PASS	.	GT	0/1
+3	9050	.	A	G	100	PASS	.	GT	0/1
+3	9100	.	A	G	100	PASS	.	GT	0/1
+3	9150	.	A	G	100	PASS	.	GT	0/1
+3	9200	.	A	G	100	PASS	.	GT	0/1
+3	9250	.	A	G	100	PASS	.	GT	0/1
+3	9300	.	A	G	100	PASS	.	GT	0/1
+3	9350	.	A	G	100	PASS	.	GT	0/1
+3	9400	.	A	G	100	PASS	.	GT	0/1
+3	9450	.	A	G	100	PASS	.	GT	0/1
+3	9500	.	A	G	100	PASS	.	GT	0/1
+3	9550	.	A	G	100	PASS	.	GT	0/1
+3	9600	.	A	G	100	PASS	.	GT	0/1
+3	9650	.	A	G	100	PASS	.	GT	0/1
+3	9700	.	A	G	100	PASS	.	GT	0/1
+3	9750	.	A	G	100	PASS	.	GT	0/1
+3	9800	.	A	G	100	PASS	.	GT	0/1
+3	9850	.	A	G	100	PASS	.	GT	0/1
+3	9900	.	A	G	100	PASS	.	GT	0/1
+3	9950	.	A	G	100	PASS	.	GT	0/1
+3	10000	.	A	G	100	PASS	.	GT	0/1
+3	10050	.	A	G	100	PASS	.	GT	0/1
diff --git a/test/test.pl b/test/test.pl
index f67c53f30..f16cd95ec 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -426,6 +426,12 @@
 run_test(\&test_vcf_view,$opts,in=>'idx.4',out=>'idx.4.out',args=>q[-H -R {PATH}/idx.4.bed]);
 run_test(\&test_vcf_view,$opts,in=>'view-t',out=>'view-t.1.out',args=>'-Ht 2',reg=>'');
 run_test(\&test_vcf_view,$opts,in=>'view-t',out=>'view-t.2.out',args=>'-Ht 3',reg=>'');
+# Regression for samtools/bcftools#2557. The fixture has 300 single-base
+# BED entries (> htslib SNIFF_LINES=256) at dense ~100bp spacing, so the
+# htslib sniffer accepts it and the opt routes -R FILE through the
+# streaming-targets path. All three modes (fastpath, --no-regions-fastpath,
+# -T) must produce the same expected output.
+run_test(\&test_vcf_view_regions_fastpath,$opts,in=>'regions-fastpath',bed=>'regions-fastpath',out=>'regions-fastpath.out');
 run_test(\&test_vcf_view,$opts,in=>'overlap',out=>'overlap.0.out',args=>q[-H -r chr1:100-200 --regions-overlap 0]);
 run_test(\&test_vcf_view,$opts,in=>'overlap',out=>'overlap.1.out',args=>q[-H -r chr1:100-200 --regions-overlap 1]);
 run_test(\&test_vcf_view,$opts,in=>'overlap',out=>'overlap.2.out',args=>q[-H -r chr1:100-200 --regions-overlap 2]);
@@ -1701,6 +1707,25 @@ sub test_vcf_view
         test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $args{args} $$opts{tmp}/$args{in}.vcf.gz $args{reg} | $$opts{bin}/bcftools view | grep -v ^##bcftools_", exp_fix=>1);
     }
 }
+sub test_vcf_view_regions_fastpath
+{
+    # Regression test for samtools/bcftools#2557. bcftools view -R FILE
+    # opts into BCF_SR_AUTO_TARGETS_FROM_REGIONS in htslib when no -T is
+    # given, which routes a dense single-base BED through the streaming-
+    # targets path (300x+ faster than per-region tabix seeks at panel
+    # sizes). All three modes must produce the same output:
+    #   - fastpath (default, opt enabled, sniffer accepts the 300-entry BED)
+    #   - slow path (--no-regions-fastpath; suppresses the opt)
+    #   - -T FILE   (control: existing streaming-targets path)
+    my ($opts,%args) = @_;
+    bgzip_tabix_vcf($opts, $args{in});
+    bgzip_tabix($opts, file=>$args{bed}, suffix=>'bed');
+    my $vcf = "$$opts{tmp}/$args{in}.vcf.gz";
+    my $bed = "$$opts{tmp}/$args{bed}.bed.gz";
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view --no-version -H -R $bed $vcf");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view --no-version -H -R $bed --no-regions-fastpath $vcf");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view --no-version -H -T $bed $vcf");
+}
 sub test_vcf_64bit
 {
     my ($opts,%args) = @_;
diff --git a/vcfview.c b/vcfview.c
index e830e96a1..6feb35385 100644
--- a/vcfview.c
+++ b/vcfview.c
@@ -67,6 +67,7 @@ typedef struct _args_t
     bcf_hdr_t *hdr, *hnull, *hsub; // original header, sites-only header, subset header
     char **argv, *format, *sample_names, *subset_fname, *targets_list, *regions_list;
     int regions_overlap, targets_overlap;
+    int regions_fastpath_disabled;  // --no-regions-fastpath suppresses the htslib opt-in (#2557)
     int argc, clevel, n_threads, output_type, print_header, update_info, header_only, n_samples, *imap, calc_ac;
     int trim_alts, sites_only, known, novel, min_alleles, max_alleles, private_vars, uncalled, phased;
     int min_ac, min_ac_type, max_ac, max_ac_type, min_af_type, max_af_type, gt_type;
@@ -521,6 +522,7 @@ static void usage(args_t *args)
     fprintf(stderr, "    -r, --regions REGION              Restrict to comma-separated list of regions\n");
     fprintf(stderr, "    -R, --regions-file FILE           Restrict to regions listed in FILE\n");
     fprintf(stderr, "        --regions-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
+    fprintf(stderr, "        --no-regions-fastpath         Disable the dense-single-base BED auto-promotion (#2557); always index-jump\n");
     fprintf(stderr, "    -t, --targets [^]REGION           Similar to -r but streams rather than index-jumps. Exclude regions with \"^\" prefix\n");
     fprintf(stderr, "    -T, --targets-file [^]FILE        Similar to -R but streams rather than index-jumps. Exclude regions with \"^\" prefix\n");
     fprintf(stderr, "        --targets-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [0]\n");
@@ -611,6 +613,7 @@ int main_vcfview(int argc, char *argv[])
         {"regions",required_argument,NULL,'r'},
         {"regions-file",required_argument,NULL,'R'},
         {"regions-overlap",required_argument,NULL,3},
+        {"no-regions-fastpath",no_argument,NULL,11},
         {"min-ac",required_argument,NULL,'c'},
         {"max-ac",required_argument,NULL,'C'},
         {"min-af",required_argument,NULL,'q'},
@@ -755,6 +758,7 @@ int main_vcfview(int argc, char *argv[])
             case 10 :
                 if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
                 break;
+            case 11 : args->regions_fastpath_disabled = 1; break;
 
             case 'W':
                 if (!(args->write_index = write_index_parse(optarg)))
@@ -784,6 +788,15 @@ int main_vcfview(int argc, char *argv[])
     if ( args->regions_list )
     {
         bcf_sr_set_opt(args->files,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
+        // #2557: opt into the htslib dense-single-base auto-promotion when
+        // the regions are a file AND no -T is set (BCF_SR_AUTO_TARGETS_FROM_REGIONS
+        // populates readers->targets, which conflicts with a subsequent
+        // bcf_sr_set_targets() call). The htslib sniffer decides per-file
+        // whether the file actually qualifies for the streaming-targets path;
+        // sparse / small / wide BEDs fall back to the seek-per-region default.
+        // --no-regions-fastpath suppresses the opt unconditionally.
+        if ( regions_is_file && !args->targets_list && !args->regions_fastpath_disabled )
+            bcf_sr_set_opt(args->files, BCF_SR_AUTO_TARGETS_FROM_REGIONS);
         if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
             error("Failed to read the regions: %s\n", args->regions_list);
     }