| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | ssw.hpp | 178 static inline char cigar_int_to_op(uint32_t cigar_int) in cigar_int_to_op() argument
180 return (cigar_int & 0xfU) > 8 ? 'M': MAPSTR[cigar_int & 0xfU]; in cigar_int_to_op()
189 static inline uint32_t cigar_int_to_len (uint32_t cigar_int) in cigar_int_to_len() argument
191 return cigar_int >> BAM_CIGAR_SHIFT; in cigar_int_to_len()
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| /dports/biology/canu/canu-2.2/src/utility/src/utility/ |
| H A D | align-ssw.H | 190 static inline char cigar_int_to_op(uint32_t cigar_int) { in cigar_int_to_op() argument
191 return (cigar_int & 0xfU) > 8 ? 'M': MAPSTR[cigar_int & 0xfU]; in cigar_int_to_op()
198 static inline uint32_t cigar_int_to_len (uint32_t cigar_int) { in cigar_int_to_len() argument
199 return cigar_int >> BAM_CIGAR_SHIFT; in cigar_int_to_len()
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/SeqLib/ |
| H A D | ssw.h | 168 static inline char cigar_int_to_op(uint32_t cigar_int) in cigar_int_to_op() argument
170 return (cigar_int & 0xfU) > 8 ? 'M': MAPSTR[cigar_int & 0xfU]; in cigar_int_to_op()
179 static inline uint32_t cigar_int_to_len (uint32_t cigar_int) in cigar_int_to_len() argument
181 return cigar_int >> BAM_CIGAR_SHIFT; in cigar_int_to_len()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | ssw.hpp | 169 static inline char cigar_int_to_op(uint32_t cigar_int) in cigar_int_to_op() argument
171 return (cigar_int & 0xfU) > 8 ? 'M': MAPSTR[cigar_int & 0xfU]; in cigar_int_to_op()
180 static inline uint32_t cigar_int_to_len (uint32_t cigar_int) in cigar_int_to_len() argument
182 return cigar_int >> BAM_CIGAR_SHIFT; in cigar_int_to_len()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | ssw.hpp | 169 static inline char cigar_int_to_op(uint32_t cigar_int) in cigar_int_to_op() argument
171 return (cigar_int & 0xfU) > 8 ? 'M': MAPSTR[cigar_int & 0xfU]; in cigar_int_to_op()
180 static inline uint32_t cigar_int_to_len (uint32_t cigar_int) in cigar_int_to_len() argument
182 return cigar_int >> BAM_CIGAR_SHIFT; in cigar_int_to_len()
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| /dports/biology/canu/canu-2.2/src/utility/src/parasail/ |
| H A D | cigar.c | 105 char parasail_cigar_decode_op(uint32_t cigar_int) { in parasail_cigar_decode_op() argument
106 return (cigar_int & 0xfU) > 9 ? 'M': BAM_CIGAR_STR[cigar_int & 0xfU]; in parasail_cigar_decode_op()
109 uint32_t parasail_cigar_decode_len(uint32_t cigar_int) { in parasail_cigar_decode_len() argument
110 return cigar_int >> BAM_CIGAR_SHIFT; in parasail_cigar_decode_len()
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| H A D | parasail.h | 390 extern char parasail_cigar_decode_op(uint32_t cigar_int);
399 extern uint32_t parasail_cigar_decode_len(uint32_t cigar_int);
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| /dports/biology/mmseqs2/MMseqs2-13-45111/src/alignment/ |
| H A D | StripedSmithWaterman.h | 176 static char cigar_int_to_op (uint32_t cigar_int);
178 static uint32_t cigar_int_to_len (uint32_t cigar_int);
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| H A D | StripedSmithWaterman.cpp | 274 char SmithWaterman::cigar_int_to_op(uint32_t cigar_int) { in cigar_int_to_op() argument
275 uint8_t letter_code = cigar_int & 0xfU; in cigar_int_to_op()
295 uint32_t SmithWaterman::cigar_int_to_len (uint32_t cigar_int) in cigar_int_to_len() argument
297 uint32_t res = cigar_int >> 4; in cigar_int_to_len()
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| /dports/biology/subread/subread-2.0.2-source/src/longread-one/ |
| H A D | LRMfile-io.c | 203 int LRMgenerate_bam_record_encode_cigar(LRMcontext_t * context, int * cigar_int, char * cigar, int … in LRMgenerate_bam_record_encode_cigar() argument
225 cigar_int[num_opt ++] = (tmp_int << 4) | int_opt; in LRMgenerate_bam_record_encode_cigar()
230 cigar_int[num_opt ++] = (tmp_int << 4) | int_opt; in LRMgenerate_bam_record_encode_cigar()
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| /dports/biology/subread/subread-2.0.2-source/src/ |
| H A D | sambam-file.h | 221 int SamBam_compress_cigar(char * cigar, int * cigar_int, int * ret_coverage, int max_secs);
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| H A D | sambam-file.c | 1427 int SamBam_compress_cigar(char * cigar, int * cigar_int, int * ret_coverage, int max_secs) in SamBam_compress_cigar() argument
1450 cigar_int[num_opt ++] = (tmp_int << 4) | int_opt; in SamBam_compress_cigar()
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