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_vars.mk src/htslib/htslib_vars.mk
new file mode 100644
index 0000000..05e2a80
--- /dev/null
+++ src/htslib/htslib_vars.mk
@@ -0,0 +1,49 @@
+# Makefile variables useful for third-party code using htslib's public API.
+#
+#    Copyright (C) 2013-2015 Genome Research Ltd.
+#
+#    Author: John Marshall <jm18@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.
+
+# These variables can be used to express dependencies on htslib headers.
+# See htslib.mk for details.
+
+htslib_bgzf_h = $(HTSPREFIX)htslib/bgzf.h
+htslib_cram_h = $(HTSPREFIX)htslib/cram.h $(htslib_hts_h)
+htslib_faidx_h = $(HTSPREFIX)htslib/faidx.h $(htslib_hts_defs_h)
+htslib_hfile_h = $(HTSPREFIX)htslib/hfile.h $(htslib_hts_defs_h)
+htslib_hts_h = $(HTSPREFIX)htslib/hts.h
+htslib_hts_defs_h = $(HTSPREFIX)htslib/hts_defs.h
+htslib_kbitset_h = $(HTSPREFIX)htslib/kbitset.h
+htslib_kfunc_h = $(HTSPREFIX)htslib/kfunc.h
+htslib_khash_h = $(HTSPREFIX)htslib/khash.h
+htslib_khash_str2int_h = $(HTSPREFIX)htslib/khash_str2int.h $(htslib_khash_h)
+htslib_klist_h = $(HTSPREFIX)htslib/klist.h
+htslib_knetfile_h = $(HTSPREFIX)htslib/knetfile.h
+htslib_kseq_h = $(HTSPREFIX)htslib/kseq.h
+htslib_ksort_h = $(HTSPREFIX)htslib/ksort.h
+htslib_kstring_h = $(HTSPREFIX)htslib/kstring.h
+htslib_regidx_h = $(HTSPREFIX)htslib/regidx.h
+htslib_sam_h = $(HTSPREFIX)htslib/sam.h $(htslib_hts_h)
+htslib_synced_bcf_reader_h = $(HTSPREFIX)htslib/synced_bcf_reader.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_tbx_h)
+htslib_tbx_h = $(HTSPREFIX)htslib/tbx.h $(htslib_hts_h)
+htslib_vcf_h = $(HTSPREFIX)htslib/vcf.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_hts_defs_h)
+htslib_vcf_sweep_h = $(HTSPREFIX)htslib/vcf_sweep.h $(htslib_hts_h) $(htslib_vcf_h)
+htslib_vcfutils_h = $(HTSPREFIX)htslib/vcfutils.h $(htslib_vcf_h)