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Searched refs:SamBam_FILE (Results 1 – 12 of 12) sorted by relevance

/dports/biology/subread/subread-2.0.2-source/src/
H A Dsambam-file.h97 } SamBam_FILE; typedef
170 SamBam_FILE * SamBam_fopen(char * fname , int file_type);
173 void SamBam_fclose(SamBam_FILE * fp);
178 int SamBam_feof(SamBam_FILE * fp);
195 char * SamBam_fgets(SamBam_FILE * fp , char * buff , int buff_len , int seq_needed);
219 int SamBam_fetch_next_chunk(SamBam_FILE *fp);
H A DsamMappedBases.c49 SamBam_FILE * in_fp = SamBam_fopen(fn,context->is_BAM?SAMBAM_FILE_BAM:SAMBAM_FILE_SAM); in countBases()
H A Dsambam-file.c42 int SamBam_fetch_next_chunk(SamBam_FILE *fp) in SamBam_fetch_next_chunk()
97 SamBam_FILE * sambam_reader; in is_paired_end_BAM()
111 SamBam_FILE * SamBam_fopen(char * fname , int file_type) in SamBam_fopen()
113 SamBam_FILE * ret = (SamBam_FILE *)malloc(sizeof(SamBam_FILE)); in SamBam_fopen()
114 memset(ret, 0, sizeof(SamBam_FILE)); in SamBam_fopen()
223 void SamBam_fclose(SamBam_FILE * fp) in SamBam_fclose()
239 int SamBam_feof(SamBam_FILE * fp) in SamBam_feof()
246 void SamBam_read_ref_info(SamBam_FILE * ret) in SamBam_read_ref_info()
289 char * SamBam_fgets(SamBam_FILE * fp, char * buff , int buff_len, int seq_needed) in SamBam_fgets()
1080 SamBam_FILE * fp = SamBam_fopen(argv[1], SAMBAM_FILE_BAM); in test_bamview()
H A Dpropmapped.c134 …SamBam_FILE * in_fp = SamBam_fopen(context -> input_file_name ,context -> is_BAM_input?SAMBAM_FIL… in propMapped()
329 …SamBam_FILE * in_fp = SamBam_fopen(context -> input_file_name ,context -> is_BAM_input?SAMBAM_FIL… in split_PE_sambam()
H A Dsubtools.c93 SamBam_FILE * in_fp = SamBam_fopen(in_name,in_SAM?SAMBAM_FILE_SAM:SAMBAM_FILE_BAM); in main()
H A DremoveDupReads.c159 …SamBam_FILE * fp = SamBam_fopen(in_SAM_file, input_file_type==FILE_TYPE_BAM?SAMBAM_FILE_BAM:SAMBAM… in report_remainder()
H A Dcoverage_calc.c162 SamBam_FILE * in_fp = SamBam_fopen(input_file_name, is_BAM_input?SAMBAM_FILE_BAM:SAMBAM_FILE_SAM); in covCalc()
H A DqualityScores.c48 SamBam_FILE * sambam_reader;
H A Dglobal-reassembly.c388 SamBam_FILE * reader = NULL; in GRA_trim_reads()
H A Dinput-files.c1597 SamBam_FILE * fp = SamBam_fopen(in_SAM_file,is_BAM?SAMBAM_FILE_BAM:SAMBAM_FILE_SAM); in get_known_chromosomes()
1841 SamBam_FILE * sambam_reader; in break_SAM_file()
6691 … SamBam_FILE * tpfp = SamBam_fopen(fname, (FILE_TYPE_BAM == ret)?SAMBAM_FILE_BAM:SAMBAM_FILE_SAM); in probe_file_type_EX()
H A DHelperFunctions.c721 …SamBam_FILE * bamfp = SamBam_fopen("/usr/local/work/liao/arena/Rsubread_Paper_OCT2016/RNAseq-SimHG… in test_bam_reader()
H A Dcore.c927 SamBam_FILE * sambam_reader;