--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/test/test-vcf-api.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,282 @@
+/*  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;
+}
+