11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/htslib/test/test-vcf-sweep.c src/htslib/test/test-vcf-sweep.c
new file mode 100644
index 0000000..57c47bc
--- /dev/null
+++ src/htslib/test/test-vcf-sweep.c
@@ -0,0 +1,112 @@
+/*  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;
+}
+
+