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

diff --git src/htslib/config.mk src/htslib/config.mk
deleted file mode 100644
index a2b091712d0..00000000000
--- src/htslib/config.mk
+++ /dev/null
@@ -1,111 +0,0 @@
-#  Optional configure Makefile overrides for htslib.
-#
-#    Copyright (C) 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.
-
-# This is config.mk.  Generated from config.mk.in by configure.
-#
-# If you use configure, this file overrides variables and augments rules
-# in the Makefile to reflect your configuration choices.  If you don't run
-# configure, the main Makefile contains suitable conservative defaults.
-
-prefix       = /usr/local
-exec_prefix  = ${prefix}
-bindir       = ${exec_prefix}/bin
-includedir   = ${prefix}/include
-libdir       = ${exec_prefix}/lib
-libexecdir   = ${exec_prefix}/libexec
-datarootdir  = ${prefix}/share
-mandir       = ${datarootdir}/man
-
-#CC     = gcc34
-RANLIB = ranlib
-
-CPPFLAGS = 
-#CFLAGS   = -g -O2
-LDFLAGS  = 
-LIBS     = 
-
-# Lowercase here indicates these are "local" to config.mk
-plugin_OBJS =
-noplugin_LDFLAGS =
-noplugin_LIBS =
-
-# ifeq/.../endif, +=, and target-specific variables are GNU Make-specific.
-# If you don't have GNU Make, comment out this conditional and note that
-# to enable iRODS you will need to implement the following elsewhere.
-ifeq "iRODS-disabled" "iRODS-enabled"
-
-IRODS_HOME ?= /disabled
-
-IRODS_CPPFLAGS = \
-	-I$(IRODS_HOME)/lib/api/include \
-	-I$(IRODS_HOME)/lib/core/include \
-	-I$(IRODS_HOME)/lib/md5/include \
-	-I$(IRODS_HOME)/lib/sha1/include \
-	-I$(IRODS_HOME)/server/core/include \
-	-I$(IRODS_HOME)/server/drivers/include \
-	-I$(IRODS_HOME)/server/icat/include
-
-IRODS_LDFLAGS = -L$(IRODS_HOME)/lib/core/obj
-IRODS_LIBS = -lRodsAPIs -lgssapi_krb5
-
-plugin_OBJS += hfile_irods.o
-
-hfile_irods.o hfile_irods.pico: CPPFLAGS += $(IRODS_CPPFLAGS)
-hfile_irods.so hfile_irods.bundle: LDFLAGS += $(IRODS_LDFLAGS)
-hfile_irods.so hfile_irods.bundle: LIBS += $(IRODS_LIBS)
-
-noplugin_LDFLAGS += $(IRODS_LDFLAGS)
-noplugin_LIBS += $(IRODS_LIBS)
-
-endif
-
-ifeq "libcurl-disabled" "libcurl-enabled"
-
-LIBCURL_LIBS = -lcurl 
-
-plugin_OBJS += hfile_libcurl.o
-
-hfile_libcurl.so hfile_libcurl.bundle: LIBS += $(LIBCURL_LIBS)
-
-noplugin_LIBS += $(LIBCURL_LIBS)
-
-endif
-
-ifeq "plugins-no" "plugins-yes"
-
-plugindir  = $(libexecdir)/htslib
-pluginpath = $(libexecdir)/htslib
-
-LIBHTS_OBJS += plugin.o
-PLUGIN_OBJS += $(plugin_OBJS)
-
-plugin.o plugin.pico: CPPFLAGS += -DPLUGINPATH=\"$(pluginpath)\"
-
-else
-
-LIBHTS_OBJS += $(plugin_OBJS)
-LDFLAGS += $(noplugin_LDFLAGS)
-LIBS += $(noplugin_LIBS)
-
-endif