1 /*=========================================================================== 2 * 3 * PUBLIC DOMAIN NOTICE 4 * National Center for Biotechnology Information 5 * 6 * This software/database is a "United States Government Work" under the 7 * terms of the United States Copyright Act. It was written as part of 8 * the author's official duties as a United States Government employee and 9 * thus cannot be copyrighted. This software/database is freely available 10 * to the public for use. The National Library of Medicine and the U.S. 11 * Government have not placed any restriction on its use or reproduction. 12 * 13 * Although all reasonable efforts have been taken to ensure the accuracy 14 * and reliability of the software and data, the NLM and the U.S. 15 * Government do not and cannot warrant the performance or results that 16 * may be obtained by using this software or data. The NLM and the U.S. 17 * Government disclaim all warranties, express or implied, including 18 * warranties of performance, merchantability or fitness for any particular 19 * purpose. 20 * 21 * Please cite the author in any work or product based on this material. 22 * 23 * =========================================================================== 24 * 25 */ 26 27 #ifndef _h_csra1_reference_window_ 28 #define _h_csra1_reference_window_ 29 30 #ifndef _h_kfc_defs_ 31 #include <kfc/defs.h> 32 #endif 33 34 #ifdef __cplusplus 35 extern "C" { 36 #endif 37 38 /*-------------------------------------------------------------------------- 39 * forwards 40 */ 41 42 struct NGS_Cursor; 43 struct NGS_Alignment; 44 struct NGS_ReadCollection; 45 46 struct NGS_Alignment * CSRA1_ReferenceWindowMake ( ctx_t ctx, 47 struct NGS_ReadCollection * coll, 48 const struct NGS_Cursor* curs, 49 bool circular, 50 uint64_t ref_length, 51 uint32_t chunk_size, 52 int64_t primary_begin_row, 53 int64_t secondary_begin_row, 54 int64_t end_row, 55 uint64_t offset, 56 uint64_t size, /* 0 - all remaining */ 57 bool wants_primary, 58 bool wants_secondary, 59 uint32_t filters, 60 int32_t map_qual, 61 uint64_t id_offset ); 62 63 #ifdef __cplusplus 64 } 65 #endif 66 67 #endif /* _h_csra1_alignment_ */ 68