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- /* samtools.h -- utility routines.
-
- Copyright (C) 2013-2015, 2019 Genome Research Ltd.
-
- Author: Petr Danecek <pd3@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 SAMTOOLS_H
- #define SAMTOOLS_H
-
- #include "htslib/hts_defs.h"
- #include "htslib/sam.h"
-
- const char *samtools_version(void);
-
- #define CHECK_PRINTF(fmt,args) HTS_FORMAT(HTS_PRINTF_FMT, (fmt), (args))
-
- void print_error(const char *subcommand, const char *format, ...) CHECK_PRINTF(2, 3);
- void print_error_errno(const char *subcommand, const char *format, ...) CHECK_PRINTF(2, 3);
-
- void check_sam_close(const char *subcmd, samFile *fp, const char *fname, const char *null_fname, int *retp);
-
- /* Utility functions to register an output htsFile/samFile/vcfFile that
- * might be stdout. If FNAME is "-" or NULL, records FP so that print_error()
- * et al can automatically flush it before printing an error message.
- */
- void autoflush_if_stdout(htsFile *fp, const char *fname);
-
- /* Call this before closing FP; check_sam_close() does this automatically.
- */
- void release_autoflush(htsFile *fp);
-
- /*
- * Utility function to add an index to a file we've opened for write.
- * NB: Call this after writing the header and before writing sequences.
- *
- * The returned index filename should be freed by the caller, but only
- * after sam_idx_save has been called.
- *
- * Returns index filename on success,
- * NULL on failure.
- */
- char *auto_index(htsFile *fp, const char *fn, bam_hdr_t *header);
-
- #endif
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