7df6e18265341f87a69fba808aa1f92f8ebca841
markd
  Wed Apr 15 13:39:42 2026 -0700
move copy of htslib

diff --git src/htslib/htslib_vars.mk src/htslib/htslib_vars.mk
deleted file mode 100644
index 05e2a8076b6..00000000000
--- src/htslib/htslib_vars.mk
+++ /dev/null
@@ -1,49 +0,0 @@
-# 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)