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/faidx.h src/htslib/htslib/faidx.h
new file mode 100644
index 0000000..f44bf00
--- /dev/null
+++ src/htslib/htslib/faidx.h
@@ -0,0 +1,137 @@
+/* faidx.h -- FASTA random access.
+
+   Copyright (C) 2008, 2009, 2013, 2014 Genome Research Ltd.
+
+   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_FAIDX_H
+#define HTSLIB_FAIDX_H
+
+#include "hts_defs.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*!
+  @header
+
+  Index FASTA files and extract subsequence.
+
+  The fai file index columns are:
+    - chromosome name
+    - chromosome length: number of bases
+    - offset: number of bytes to skip to get to the first base
+        from the beginning of the file, including the length
+        of the sequence description string (">chr ..\n")
+    - line length: number of bases per line (excluding \n)
+    - binary line length: number of bytes, including \n
+
+  @copyright The Wellcome Trust Sanger Institute.
+ */
+
+struct __faidx_t;
+typedef struct __faidx_t faidx_t;
+
+    /*!
+      @abstract   Build index for a FASTA or bgzip-compressed FASTA file.
+      @param  fn  FASTA file name
+      @return     0 on success; or -1 on failure
+      @discussion File "fn.fai" will be generated.
+     */
+    int fai_build(const char *fn);
+
+    /*!
+      @abstract    Destroy a faidx_t struct.
+      @param  fai  Pointer to the struct to be destroyed
+     */
+    void fai_destroy(faidx_t *fai);
+
+    /*!
+      @abstract   Load index from "fn.fai".
+      @param  fn  File name of the FASTA file
+     */
+    faidx_t *fai_load(const char *fn);
+
+    /*!
+      @abstract    Fetch the sequence in a region.
+      @param  fai  Pointer to the faidx_t struct
+      @param  reg  Region in the format "chr2:20,000-30,000"
+      @param  len  Length of the region; -2 if seq not present, -1 general error
+      @return      Pointer to the sequence; null on failure
+
+      @discussion The returned sequence is allocated by malloc family
+      and should be destroyed by end users by calling free() on it.
+     */
+    char *fai_fetch(const faidx_t *fai, const char *reg, int *len);
+
+    /*!
+      @abstract    Fetch the number of sequences.
+      @param  fai  Pointer to the faidx_t struct
+      @return      The number of sequences
+     */
+    int faidx_fetch_nseq(const faidx_t *fai) HTS_DEPRECATED("Please use faidx_nseq instead");
+
+    /*!
+      @abstract    Fetch the sequence in a region.
+      @param  fai  Pointer to the faidx_t struct
+      @param  c_name Region name
+      @param  p_beg_i  Beginning position number (zero-based)
+      @param  p_end_i  End position number (zero-based)
+      @param  len  Length of the region; -2 if c_name not present, -1 general error
+      @return      Pointer to the sequence; null on failure
+
+      @discussion The returned sequence is allocated by malloc family
+      and should be destroyed by end users by calling free() on it.
+     */
+    char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
+
+    /*!
+      @abstract    Query if sequence is present
+      @param  fai  Pointer to the faidx_t struct
+      @param  seq  Sequence name
+      @return      1 if present or 0 if absent
+     */
+    int faidx_has_seq(const faidx_t *fai, const char *seq);
+
+    /*!
+      @abstract    Return number of sequences in fai index
+     */
+    int faidx_nseq(const faidx_t *fai);
+
+    /*!
+      @abstract    Return name of i-th sequence
+     */
+    const char *faidx_iseq(const faidx_t *fai, int i);
+
+    /*!
+      @abstract    Return sequence length, -1 if not present
+     */
+    int faidx_seq_len(const faidx_t *fai, const char *seq);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif