7df6e18265341f87a69fba808aa1f92f8ebca841
markd
  Wed Apr 15 13:39:42 2026 -0700
move copy of htslib

diff --git src/htslib/test/test-vcf-sweep.c src/htslib/test/test-vcf-sweep.c
deleted file mode 100644
index 57c47bc3302..00000000000
--- src/htslib/test/test-vcf-sweep.c
+++ /dev/null
@@ -1,112 +0,0 @@
-/*  test/test-vcf-sweep.c -- VCF test harness.
-
-    Copyright (C) 2013 Genome Research Ltd.
-
-    Author: Petr Danecek <pd3@sanger.ac.uk>
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
-THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE.  */
-
-#include <stdio.h>
-#include <htslib/vcf_sweep.h>
-
-int main(int argc, char **argv)
-{
-    if ( argc!=2 )
-    {
-        fprintf(stderr,"Usage: test-vcf-sweep <file.bcf|file.vcf>\n");
-        return 1;
-    }
-
-    // Init variables. The checksum is just for this test program to output
-    // something and verify that all sites are read in both passes - fwd and
-    // bwd.
-    bcf_sweep_t *sw = bcf_sweep_init(argv[1]);
-    bcf_hdr_t *hdr  = bcf_sweep_hdr(sw);
-    int chksum = 0;
-
-    // First we must sweep forward and read the whole file to build an index.
-    // If this is undesirable, we can require the presence of a .gzi index
-    // which can be created with `bgzip -r` from the samtools/htslib package
-    bcf1_t *rec;
-    while ( (rec = bcf_sweep_fwd(sw)) ) chksum += rec->pos+1;
-    printf("fwd position chksum: %d\n", chksum);
-
-    // Now sweep backward.
-    chksum = 0;
-    while ( (rec = bcf_sweep_bwd(sw)) ) chksum += rec->pos+1;
-    printf("bwd position chksum: %d\n", chksum);
-
-    // And forward and backward again, this time summing the PL vectors
-    int i,j, mPLs = 0, nPLs;
-    int32_t *PLs = NULL;
-    chksum = 0;
-    while ( (rec = bcf_sweep_fwd(sw)) )
-    {
-        // get copy of the PL vectors
-        nPLs = bcf_get_format_int32(hdr, rec, "PL", &PLs, &mPLs);
-        if ( !nPLs ) continue;  // PL not present
-
-        // how many values are there per sample
-        int nvals = nPLs / bcf_hdr_nsamples(hdr);
-
-        int32_t *ptr = PLs;
-        for (i=0; i<bcf_hdr_nsamples(hdr); i++)
-        {
-            for (j=0; j<nvals; j++)
-            {
-                // check for shorter vectors (haploid genotypes amongst diploids)
-                if ( ptr[j]==bcf_int32_vector_end ) break;
-
-                // skip missing values
-                if ( ptr[j]==bcf_int32_missing ) continue;
-
-                chksum += ptr[j];
-            }
-            ptr += nvals;
-        }
-    }
-    printf("fwd PL chksum: %d\n", chksum);
-
-    // And the same backwards..
-    chksum = 0;
-    while ( (rec = bcf_sweep_bwd(sw)) )
-    {
-        nPLs = bcf_get_format_int32(hdr, rec, "PL", &PLs, &mPLs);
-        if ( !nPLs ) continue;
-        int nvals = nPLs / bcf_hdr_nsamples(hdr);
-        int32_t *ptr = PLs;
-        for (i=0; i<bcf_hdr_nsamples(hdr); i++)
-        {
-            for (j=0; j<nvals; j++)
-            {
-                if ( ptr[j]==bcf_int32_vector_end ) break;
-                if ( ptr[j]==bcf_int32_missing ) continue;
-                chksum += ptr[j];
-            }
-            ptr += nvals;
-        }
-    }
-    printf("bwd PL chksum: %d\n", chksum);
-
-    // Clean up
-    bcf_sweep_destroy(sw);
-    return 0;
-}
-
-