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 #ifndef _tools_cg_load_defs_h_ 27 #define _tools_cg_load_defs_h_ 28 29 30 #include <stdint.h> /* uint64_t */ 31 32 33 #define CG_FORMAT_2_5 0x02050000 34 35 36 /* buffers and sizes */ 37 38 /* 39 #define CG_CHROMOSOME_NAME (8) make if fit NC_003977 */ 40 #define CG_CHROMOSOME_NAME (10) 41 42 #define CG_SLIDE (32) 43 #define CG_LANE (8) 44 45 #define CG_READS_NREADS (2) 46 47 #define CG_READS15_SPOT_LEN 70 48 #define CG_READS25_SPOT_LEN 60 49 50 #define CG_READS15_NGAPS 3 51 #define CG_READS25_NGAPS 2 52 53 #define CG_MAPPINGS_MAX (2048) 54 #define CG_EVDNC_PLOIDY (3) 55 #define CG_EVDNC_INTERVALID_LEN (32) 56 #define CG_EVDNC_SPOT_LEN (10 * 1024) 57 #define CG_TAG_LFR_DATA_LEN (10) 58 59 /* CG_EVDNC_ALLELE_NUM is 3 in v.1.5; 4 in v.2 */ 60 #define CG_EVDNC_ALLELE_NUM (4) 61 62 #define CG_EVDNC_ALLELE_LEN (10 * 1024) 63 #define CG_EVDNC_ALLELE_CIGAR_LEN (10 * 1024) 64 65 typedef char CGFIELD_LIBRARY_TYPE; 66 typedef char CGFIELD_SAMPLE_TYPE; 67 typedef char CGFIELD_SLIDE_TYPE; 68 typedef char CGFIELD_LANE_TYPE; 69 typedef char CGFIELD_CHROMOSOME_TYPE; 70 typedef char CGFIELD_ASSEMBLY_ID_TYPE; 71 typedef char CGFIELD_SOFTWARE_VERSION_TYPE; 72 typedef char CGFIELD_DBSNP_BUILD_TYPE; 73 typedef char CGFIELD_COSMIC_TYPE; 74 typedef char CGFIELD_PFAM_DATE_TYPE; 75 typedef char CGFIELD_MIRBASE_VERSION_TYPE; 76 typedef char CGFIELD_DGV_VERSION_TYPE; 77 typedef char CGFIELD_GENERATED_AT_TYPE; 78 typedef char CGFIELD_GENERATED_BY_TYPE; 79 typedef char CGFIELD_GENE_ANNOTATIONS_TYPE; 80 typedef char CGFIELD_GENOME_REFERENCE_TYPE; 81 typedef uint32_t CGFIELD_BATCH_FILE_NUMBER_TYPE; 82 typedef uint64_t CGFIELD_BATCH_OFFSET_TYPE; 83 typedef uint32_t CGFIELD_FIELD_SIZE_TYPE; 84 typedef uint32_t CGFIELD_MAX_PLOIDY_TYPE; 85 typedef uint16_t CGFIELD_WINDOW_SHIFT_TYPE; 86 typedef uint16_t CGFIELD_WINDOW_WIDTH_TYPE; 87 typedef uint16_t CGFIELD_NUMBER_LEVELS_TYPE; 88 typedef uint16_t CGFIELD_MEAN_LEVEL_X_TYPE; 89 typedef uint16_t CGFIELD_WELL_ID; 90 91 /******************************************************************************/ 92 93 typedef enum CG_EFileType_enum { 94 cg_eFileType_Unknown = 0, 95 cg_eFileType_READS = 1, 96 cg_eFileType_MAPPINGS, 97 cg_eFileType_LIB_DNB, 98 cg_eFileType_LIB_MATE_GAPS, 99 cg_eFileType_LIB_SEQDEP_GAPS, 100 cg_eFileType_REFMETRICS, 101 cg_eFileType_IDENTIFIER_MAPPING, 102 cg_eFileType_DBSNP_TO_CGI, 103 cg_eFileType_GENE_ANNOTATION, 104 cg_eFileType_SUMMARY_REPORT, 105 cg_eFileType_VAR_ANNOTATION, 106 cg_eFileType_GENE_VAR_SUMMARY_REPORT, 107 cg_eFileType_EVIDENCE_CORRELATION, 108 cg_eFileType_EVIDENCE_DNBS, 109 cg_eFileType_EVIDENCE_INTERVALS, 110 cg_eFileType_COVERAGE_DISTRIBUTION, 111 cg_eFileType_COVERAGE_BY_GC, 112 cg_eFileType_DEPTH_OF_COVERAGE, 113 cg_eFileType_INDEL_LENGTH_CODING, 114 cg_eFileType_INDEL_LENGTH, 115 cg_eFileType_SUBSTITUTION_LENGTH_CODING, 116 cg_eFileType_SUBSTITUTION_LENGTH, 117 cg_eFileType_CNV_SEGMENTS, 118 cg_eFileType_TUMOR_CNV_SEGMENTS, 119 cg_eFileType_CNV_DETAILS_SCORES, 120 cg_eFileType_TUMOR_DETAILS_SCORES, 121 cg_eFileType_NONDIPLOID_SOMATIC_CNV_SEGMENTS, 122 cg_eFileType_NONDIPLOID_SOMATIC_CNV_DETAILS, 123 cg_eFileType_JUNCTIONS, 124 cg_eFileType_JUNCTION_DNBS, 125 cg_eFileType_SV_EVENTS, 126 cg_eFileType_VAR_OLPL, 127 cg_eFileType_MEI, 128 cg_eFileType_TUMOR_CNV_DETAILS, 129 cg_eFileType_DIPLOID_SOMATIC_CNV_SEGMENTS, 130 cg_eFileType_COVERAGE_DISTRIBUTION_CODING, 131 cg_eFileType_COVERAGE_BY_GC_CODING, 132 cg_eFileType_LIB_SMALL_GAPS_ROLLUP, 133 cg_eFileType_DIPLOID_SOMATIC_CNV_DETAIL_SCORES, 134 135 cg_eFileType_TAG_LFR, 136 cg_eFileType_Last 137 } CG_EFileType; 138 139 typedef enum { 140 cg_eLibraryType_Unknown, 141 cg_eLibraryType_PureLFR, 142 cg_eLibraryType_MixedLFR, 143 cg_eLibraryType_MixedSTD, 144 cg_eLibraryType_Standard, 145 } CG_ELibraryType; 146 147 typedef enum CG_EMappingsFlags_enum { 148 cg_eLastDNBRecord = 0x01, 149 cg_eLeftHalfDnbMap = 0x00, 150 cg_eRightHalfDnbMap = 0x02, 151 cg_eFwdDnbStrand = 0x00, 152 cg_eRevDnbStrand = 0x04 153 } CG_EMappingsFlags; 154 155 typedef enum CG_EReadsFlags_enum { 156 cg_eLeftHalfDnbNoMatches = 0x01, 157 cg_eLeftHalfDnbMapOverflow = 0x02, 158 cg_eRightHalfDnbNoMatches = 0x04, 159 cg_eRightHalfDnbMapOverflow = 0x08 160 } CG_EReadsFlags; 161 162 163 #endif /* _tools_cg_load_defs_h_ */ 164