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

diff --git src/htslib/test/test-vcf-api.c src/htslib/test/test-vcf-api.c
deleted file mode 100644
index 3e7623a8982..00000000000
--- src/htslib/test/test-vcf-api.c
+++ /dev/null
@@ -1,282 +0,0 @@
-/*  test/test-vcf-api.c -- VCF test harness.
-
-    Copyright (C) 2013, 2014 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/hts.h>
-#include <htslib/vcf.h>
-#include <htslib/kstring.h>
-#include <htslib/kseq.h>
-
-void write_bcf(char *fname)
-{
-    // Init
-    htsFile *fp    = hts_open(fname,"wb");
-    bcf_hdr_t *hdr = bcf_hdr_init("w");
-    bcf1_t *rec    = bcf_init1();
-
-    // Create VCF header
-    kstring_t str = {0,0,0};
-    bcf_hdr_append(hdr, "##fileDate=20090805");
-    bcf_hdr_append(hdr, "##FORMAT=<ID=UF,Number=1,Type=Integer,Description=\"Unused FORMAT\">");
-    bcf_hdr_append(hdr, "##INFO=<ID=UI,Number=1,Type=Integer,Description=\"Unused INFO\">");
-    bcf_hdr_append(hdr, "##FILTER=<ID=Flt,Description=\"Unused FILTER\">");
-    bcf_hdr_append(hdr, "##unused=<XX=AA,Description=\"Unused generic\">");
-    bcf_hdr_append(hdr, "##unused=unformatted text 1");
-    bcf_hdr_append(hdr, "##unused=unformatted text 2");
-    bcf_hdr_append(hdr, "##contig=<ID=Unused,length=62435964>");
-    bcf_hdr_append(hdr, "##source=myImputationProgramV3.1");
-    bcf_hdr_append(hdr, "##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta");
-    bcf_hdr_append(hdr, "##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=\"Homo sapiens\",taxonomy=x>");
-    bcf_hdr_append(hdr, "##phasing=partial");
-    bcf_hdr_append(hdr, "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">");
-    bcf_hdr_append(hdr, "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">");
-    bcf_hdr_append(hdr, "##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">");
-    bcf_hdr_append(hdr, "##INFO=<ID=AA,Number=1,Type=String,Description=\"Ancestral Allele\">");
-    bcf_hdr_append(hdr, "##INFO=<ID=DB,Number=0,Type=Flag,Description=\"dbSNP membership, build 129\">");
-    bcf_hdr_append(hdr, "##INFO=<ID=H2,Number=0,Type=Flag,Description=\"HapMap2 membership\">");
-    bcf_hdr_append(hdr, "##FILTER=<ID=q10,Description=\"Quality below 10\">");
-    bcf_hdr_append(hdr, "##FILTER=<ID=s50,Description=\"Less than 50% of samples have data\">");
-    bcf_hdr_append(hdr, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
-    bcf_hdr_append(hdr, "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">");
-    bcf_hdr_append(hdr, "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">");
-    bcf_hdr_append(hdr, "##FORMAT=<ID=HQ,Number=2,Type=Integer,Description=\"Haplotype Quality\">");
-    bcf_hdr_append(hdr, "##FORMAT=<ID=TS,Number=1,Type=String,Description=\"Test String\">");
-
-    bcf_hdr_add_sample(hdr, "NA00001");
-    bcf_hdr_add_sample(hdr, "NA00002");
-    bcf_hdr_add_sample(hdr, "NA00003");
-    bcf_hdr_add_sample(hdr, NULL);      // to update internal structures
-    bcf_hdr_write(fp, hdr);
-
-
-    // Add a record
-    // 20     14370   rs6054257 G      A       29   PASS   NS=3;DP=14;AF=0.5;DB;H2           GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
-    // .. CHROM
-    rec->rid = bcf_hdr_name2id(hdr, "20");
-    // .. POS
-    rec->pos = 14369;
-    // .. ID
-    bcf_update_id(hdr, rec, "rs6054257");
-    // .. REF and ALT
-    bcf_update_alleles_str(hdr, rec, "G,A");
-    // .. QUAL
-    rec->qual = 29;
-    // .. FILTER
-    int32_t tmpi = bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS");
-    bcf_update_filter(hdr, rec, &tmpi, 1);
-    // .. INFO
-    tmpi = 3;
-    bcf_update_info_int32(hdr, rec, "NS", &tmpi, 1);
-    tmpi = 14;
-    bcf_update_info_int32(hdr, rec, "DP", &tmpi, 1);
-    float tmpf = 0.5;
-    bcf_update_info_float(hdr, rec, "AF", &tmpf, 1);
-    bcf_update_info_flag(hdr, rec, "DB", NULL, 1);
-    bcf_update_info_flag(hdr, rec, "H2", NULL, 1);
-    // .. FORMAT
-    int32_t *tmpia = (int*)malloc(bcf_hdr_nsamples(hdr)*2*sizeof(int));
-    tmpia[0] = bcf_gt_phased(0);
-    tmpia[1] = bcf_gt_phased(0);
-    tmpia[2] = bcf_gt_phased(1);
-    tmpia[3] = bcf_gt_phased(0);
-    tmpia[4] = bcf_gt_unphased(1);
-    tmpia[5] = bcf_gt_unphased(1);
-    bcf_update_genotypes(hdr, rec, tmpia, bcf_hdr_nsamples(hdr)*2);
-    tmpia[0] = 48;
-    tmpia[1] = 48;
-    tmpia[2] = 43;
-    bcf_update_format_int32(hdr, rec, "GQ", tmpia, bcf_hdr_nsamples(hdr));
-    tmpia[0] = 1;
-    tmpia[1] = 8;
-    tmpia[2] = 5;
-    bcf_update_format_int32(hdr, rec, "DP", tmpia, bcf_hdr_nsamples(hdr));
-    tmpia[0] = 51;
-    tmpia[1] = 51;
-    tmpia[2] = 51;
-    tmpia[3] = 51;
-    tmpia[4] = bcf_int32_missing;
-    tmpia[5] = bcf_int32_missing;
-    bcf_update_format_int32(hdr, rec, "HQ", tmpia, bcf_hdr_nsamples(hdr)*2);
-    char *tmp_str[] = {"String1","SomeOtherString2","YetAnotherString3"};
-    bcf_update_format_string(hdr, rec, "TS", (const char**)tmp_str, 3);
-    bcf_write1(fp, hdr, rec);
-
-    // 20     1110696 . A      G,T     67   .   NS=2;DP=10;AF=0.333,.;AA=T;DB GT 2 1   ./.
-    bcf_clear1(rec);
-    rec->rid = bcf_hdr_name2id(hdr, "20");
-    rec->pos = 1110695;
-    bcf_update_alleles_str(hdr, rec, "A,G,T");
-    rec->qual = 67;
-    tmpi = 2;
-    bcf_update_info_int32(hdr, rec, "NS", &tmpi, 1);
-    tmpi = 10;
-    bcf_update_info_int32(hdr, rec, "DP", &tmpi, 1);
-    float *tmpfa = (float*)malloc(2*sizeof(float));
-    tmpfa[0] = 0.333;
-    bcf_float_set_missing(tmpfa[1]);
-    bcf_update_info_float(hdr, rec, "AF", tmpfa, 2);
-    bcf_update_info_string(hdr, rec, "AA", "T");
-    bcf_update_info_flag(hdr, rec, "DB", NULL, 1);
-    tmpia[0] = bcf_gt_phased(2);
-    tmpia[1] = bcf_int32_vector_end;
-    tmpia[2] = bcf_gt_phased(1);
-    tmpia[3] = bcf_int32_vector_end;
-    tmpia[4] = bcf_gt_missing;
-    tmpia[5] = bcf_gt_missing;
-    bcf_update_genotypes(hdr, rec, tmpia, bcf_hdr_nsamples(hdr)*2);
-    bcf_write1(fp, hdr, rec);
-
-    free(tmpia);
-    free(tmpfa);
-
-    // Clean
-    free(str.s);
-    bcf_destroy1(rec);
-    bcf_hdr_destroy(hdr);
-    int ret;
-    if ( (ret=hts_close(fp)) )
-    {
-        fprintf(stderr,"hts_close(%s): non-zero status %d\n",fname,ret);
-        exit(ret);
-    }
-}
-
-void bcf_to_vcf(char *fname)
-{
-    htsFile *fp    = hts_open(fname,"rb");
-    bcf_hdr_t *hdr = bcf_hdr_read(fp);
-    bcf1_t *rec    = bcf_init1();
-
-    char *gz_fname = (char*) malloc(strlen(fname)+4);
-    snprintf(gz_fname,strlen(fname)+4,"%s.gz",fname);
-    htsFile *out   = hts_open(gz_fname,"wg");
-
-    bcf_hdr_t *hdr_out = bcf_hdr_dup(hdr);
-    bcf_hdr_remove(hdr_out,BCF_HL_STR,"unused");
-    bcf_hdr_remove(hdr_out,BCF_HL_GEN,"unused");
-    bcf_hdr_remove(hdr_out,BCF_HL_FLT,"Flt");
-    bcf_hdr_remove(hdr_out,BCF_HL_INFO,"UI");
-    bcf_hdr_remove(hdr_out,BCF_HL_FMT,"UF");
-    bcf_hdr_remove(hdr_out,BCF_HL_CTG,"Unused");
-    bcf_hdr_write(out, hdr_out);
-
-    while ( bcf_read1(fp, hdr, rec)>=0 )
-    {
-        bcf_write1(out, hdr_out, rec);
-
-        // Test problems caused by bcf1_sync: the data block
-        // may be realloced, also the unpacked structures must
-        // get updated.
-        bcf_unpack(rec, BCF_UN_STR);
-        bcf_update_id(hdr, rec, 0);
-        bcf_update_format_int32(hdr, rec, "GQ", NULL, 0);
-
-        bcf1_t *dup = bcf_dup(rec);     // force bcf1_sync call
-        bcf_write1(out, hdr_out, dup);
-        bcf_destroy1(dup);
-
-        bcf_update_alleles_str(hdr_out, rec, "G,A");
-        int32_t tmpi = 99;
-        bcf_update_info_int32(hdr_out, rec, "DP", &tmpi, 1);
-        int32_t tmpia[] = {9,9,9};
-        bcf_update_format_int32(hdr_out, rec, "DP", tmpia, 3);
-
-        bcf_write1(out, hdr_out, rec);
-    }
-
-    bcf_destroy1(rec);
-    bcf_hdr_destroy(hdr);
-    bcf_hdr_destroy(hdr_out);
-    int ret;
-    if ( (ret=hts_close(fp)) )
-    {
-        fprintf(stderr,"hts_close(%s): non-zero status %d\n",fname,ret);
-        exit(ret);
-    }
-    if ( (ret=hts_close(out)) )
-    {
-        fprintf(stderr,"hts_close(%s): non-zero status %d\n",gz_fname,ret);
-        exit(ret);
-    }
-
-
-    // read gzip, write stdout
-    htsFile *gz_in = hts_open(gz_fname, "r");
-    if ( !gz_in )
-    {
-        fprintf(stderr,"Could not read: %s\n", gz_fname);
-        exit(1);
-    }
-
-    kstring_t line = {0,0,0};
-    while ( hts_getline(gz_in, KS_SEP_LINE, &line)>0 )
-    {
-        kputc('\n',&line);
-        fwrite(line.s,1,line.l,stdout);
-    }
-
-    if ( (ret=hts_close(gz_in)) )
-    {
-        fprintf(stderr,"hts_close(%s): non-zero status %d\n",gz_fname,ret);
-        exit(ret);
-    }
-    free(line.s);
-    free(gz_fname);
-}
-
-void iterator(const char *fname)
-{
-    htsFile *fp = hts_open(fname, "r");
-    bcf_hdr_t *hdr = bcf_hdr_read(fp);
-    hts_idx_t *idx;
-    hts_itr_t *iter;
-
-    bcf_index_build(fname, 0);
-    idx = bcf_index_load(fname);
-
-    iter = bcf_itr_queryi(idx, bcf_hdr_name2id(hdr, "20"), 1110600, 1110800);
-    bcf_itr_destroy(iter);
-
-    iter = bcf_itr_querys(idx, hdr, "20:1110600-1110800");
-    bcf_itr_destroy(iter);
-
-    hts_idx_destroy(idx);
-    bcf_hdr_destroy(hdr);
-    int ret;
-    if ( (ret=hts_close(fp)) )
-    {
-        fprintf(stderr,"hts_close(%s): non-zero status %d\n",fname,ret);
-        exit(ret);
-    }
-}
-
-int main(int argc, char **argv)
-{
-    char *fname = argc>1 ? argv[1] : "rmme.bcf";
-    write_bcf(fname);
-    bcf_to_vcf(fname);
-    iterator(fname);
-    return 0;
-}
-