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

diff --git src/htslib/cram/misc.h src/htslib/cram/misc.h
deleted file mode 100644
index 681b28cff06..00000000000
--- src/htslib/cram/misc.h
+++ /dev/null
@@ -1,110 +0,0 @@
-/*
-Copyright (c) 1994-1997, 2001-2002 MEDICAL RESEARCH COUNCIL
-All rights reserved
-
-Redistribution and use in source and binary forms, with or without 
-modification, are permitted provided that the following conditions are met:
-
-   1 Redistributions of source code must retain the above copyright notice, 
-this list of conditions and the following disclaimer.
-
-   2 Redistributions in binary form must reproduce the above copyright notice, 
-this list of conditions and the following disclaimer in the documentation 
-and/or other materials provided with the distribution.
-
-   3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
-MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 
-promote products derived from this software without specific prior written 
-permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
-ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
-LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-/*
-Copyright (c) 2003-2013 Genome Research Ltd.
-
-Author: James Bonfield <jkb@sanger.ac.uk>
-
-Redistribution and use in source and binary forms, with or without 
-modification, are permitted provided that the following conditions are met:
-
-   1. Redistributions of source code must retain the above copyright notice, 
-this list of conditions and the following disclaimer.
-
-   2. Redistributions in binary form must reproduce the above copyright notice, 
-this list of conditions and the following disclaimer in the documentation 
-and/or other materials provided with the distribution.
-
-   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
-Institute nor the names of its contributors may be used to endorse or promote
-products derived from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
-DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-*/
-
-#ifndef _misc_h
-#define _misc_h
-
-#include "cram/os.h"
-
-#include <stdio.h>
-#include <stdarg.h>  /* varargs needed for v*printf() prototypes */
-#include <sys/types.h>
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/*
- * This informs gcc that crash() doesn't return, so it doesn't need to
- * concern itself that code paths going via crash could mean some variables
- * being undefined and then issuing uninitialised variable warnings.
- * This particularly affected convert.
- */
-#ifdef __GNUC__
-#    define __NORETURN__ __attribute__ ((__noreturn__))
-#else
-#    define __NORETURN__
-#endif
-
-/*
- * Used for printf style argument checking. We can request a function such
- * as vTcl_SetResult does argument checking, avoiding bugs with using
- * %d and passing in a 64-bit record.
- */
-#ifdef __GNUC__
-#    define __PRINTF_FORMAT__(a,b) __attribute__ ((format (printf, a, b)))
-#else
-#    define __PRINTF_FORMAT__(a,b)
-#endif
-
-extern int is_directory(char * fn);
-extern int is_file(char * fn);
-extern int file_size(char * fn);
-
-#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
-#define MAX(A,B) ( ( (A) > (B) ) ? (A) : (B) )
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /*_misc_h*/