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/htslib/tbx.h src/htslib/htslib/tbx.h
new file mode 100644
index 0000000..65243b9
--- /dev/null
+++ src/htslib/htslib/tbx.h
@@ -0,0 +1,79 @@
+/*  tbx.h -- tabix API functions.
+
+    Copyright (C) 2009, 2012-2015 Genome Research Ltd.
+    Copyright (C) 2010, 2012 Broad Institute.
+
+    Author: Heng Li <lh3@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.  */
+
+#ifndef HTSLIB_TBX_H
+#define HTSLIB_TBX_H
+
+#include "hts.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define TBX_MAX_SHIFT 31
+
+#define TBX_GENERIC 0
+#define TBX_SAM     1
+#define TBX_VCF     2
+#define TBX_UCSC    0x10000
+
+typedef struct {
+    int32_t preset;
+    int32_t sc, bc, ec; // seq col., beg col. and end col.
+    int32_t meta_char, line_skip;
+} tbx_conf_t;
+
+typedef struct {
+    tbx_conf_t conf;
+    hts_idx_t *idx;
+    void *dict;
+} tbx_t;
+
+extern tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sam, tbx_conf_vcf;
+
+    #define tbx_itr_destroy(iter) hts_itr_destroy(iter)
+    #define tbx_itr_queryi(tbx, tid, beg, end) hts_itr_query((tbx)->idx, (tid), (beg), (end), tbx_readrec)
+    #define tbx_itr_querys(tbx, s) hts_itr_querys((tbx)->idx, (s), (hts_name2id_f)(tbx_name2id), (tbx), hts_itr_query, tbx_readrec)
+    #define tbx_itr_next(htsfp, tbx, itr, r) hts_itr_next(hts_get_bgzfp(htsfp), (itr), (r), (tbx))
+    #define tbx_bgzf_itr_next(bgzfp, tbx, itr, r) hts_itr_next((bgzfp), (itr), (r), (tbx))
+
+    int tbx_name2id(tbx_t *tbx, const char *ss);
+
+    /* Internal helper function used by tbx_itr_next() */
+    BGZF *hts_get_bgzfp(htsFile *fp);
+    int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end);
+
+    int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf);
+    int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf);
+    tbx_t *tbx_index_load(const char *fn);
+    tbx_t *tbx_index_load2(const char *fn, const char *fnidx);
+    const char **tbx_seqnames(tbx_t *tbx, int *n);  // free the array but not the values
+    void tbx_destroy(tbx_t *tbx);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif