/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/test/sraxf/ |
H A D | fix_read_seg-test.cpp | 22 uint32_t nreads = 0; in TEST_CASE() local 24 fix_read_seg_impl(rs_src, nreads, 0, rs_dst); in TEST_CASE() 29 uint32_t nreads = 1; in TEST_CASE() local 36 uint32_t nreads = 1; in TEST_CASE() local 46 uint32_t nreads = 2; in TEST_CASE() local 66 uint32_t nreads = 1; in TEST_CASE() local 76 uint32_t nreads = 2; in TEST_CASE() local 88 uint32_t nreads = 1; in TEST_CASE() local 98 uint32_t nreads = 2; in TEST_CASE() local 110 uint32_t nreads = 1; in TEST_CASE() local [all …]
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/test/sraxf/ |
H A D | fix_read_seg-test.cpp | 22 uint32_t nreads = 0; in TEST_CASE() local 24 fix_read_seg_impl(rs_src, nreads, 0, rs_dst); in TEST_CASE() 29 uint32_t nreads = 1; in TEST_CASE() local 36 uint32_t nreads = 1; in TEST_CASE() local 46 uint32_t nreads = 2; in TEST_CASE() local 66 uint32_t nreads = 1; in TEST_CASE() local 76 uint32_t nreads = 2; in TEST_CASE() local 88 uint32_t nreads = 1; in TEST_CASE() local 98 uint32_t nreads = 2; in TEST_CASE() local 110 uint32_t nreads = 1; in TEST_CASE() local [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/ |
H A D | sequence-writer.c | 80 uint8_t nreads = rec->numreads; in writeRecordX() local 126 for (i = 0; i != nreads; ++i) { in writeRecordX() 157 data.nreads = nreads; in writeRecordX() 166 data.read_len.elements = nreads; in writeRecordX() 174 data.cskey.elements = nreads; in writeRecordX() 183 data.ti.elements = nreads; in writeRecordX() 204 for (i = 0; i < nreads; ++i) in totalSequenceLength() 231 for (i = 0; i != nreads; ++i) { in writeRecord2() 256 data.nreads = nreads; in writeRecord2() 273 data.cskey.elements = nreads; in writeRecord2() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/sraxf/ |
H A D | read-seg-from-readn.c | 82 assert ( * nreads != 0 ); in equal_reads_from_spot() 86 uint32_t rem = * nreads - i; in equal_reads_from_spot() 98 rslt -> elem_count = * nreads; in equal_reads_from_spot() 108 uint8_t nreads; in read_seg_from_meta() local 118 assert ( nreads > 0 ); in read_seg_from_meta() 129 if ( rd_dst[nreads-1].read_start+rd_dst[nreads-1].read_len==0) in read_seg_from_meta() 134 for(i=1;i<nreads;i++) in read_seg_from_meta() 141 else if(rd_dst[nreads-1].read_start+rd_dst[nreads-1].read_len > spot_len) in read_seg_from_meta() 144 for(i=0;i<nreads;i++) in read_seg_from_meta() 157 rslt -> elem_count = nreads; in read_seg_from_meta() [all …]
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H A D | spot-filter.c | 133 for (i = 0; i < nreads; ++i) { in check_quality() 174 , unsigned const nreads in check_dna() argument 181 for (i = 0; i < nreads; ++i) { in check_dna() 224 , unsigned const nreads in check_4na() argument 231 for (i = 0; i < nreads; ++i) { in check_4na() 267 , unsigned const nreads in check_x2na() argument 274 for (i = 0; i < nreads; ++i) { in check_x2na() 307 , unsigned const nreads in check_2na() argument 314 for (i = 0; i < nreads; ++i) { in check_2na() 485 for (i = 0; i < nreads; ++i) { in read_filter_array_to_bitset() [all …]
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H A D | fix_read_seg_impl.h | 38 static void fix_read_seg_impl(const uint16_t *rs_src, uint32_t nreads, in fix_read_seg_impl() argument 41 const uint32_t nreads2 = nreads + nreads; in fix_read_seg_impl() 56 if ( nreads == 1 ) in fix_read_seg_impl() 64 double flen = ( double ) spot_len / nreads; in fix_read_seg_impl()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/sraxf/ |
H A D | read-seg-from-readn.c | 82 assert ( * nreads != 0 ); in equal_reads_from_spot() 86 uint32_t rem = * nreads - i; in equal_reads_from_spot() 98 rslt -> elem_count = * nreads; in equal_reads_from_spot() 108 uint8_t nreads; in read_seg_from_meta() local 118 assert ( nreads > 0 ); in read_seg_from_meta() 129 if ( rd_dst[nreads-1].read_start+rd_dst[nreads-1].read_len==0) in read_seg_from_meta() 134 for(i=1;i<nreads;i++) in read_seg_from_meta() 141 else if(rd_dst[nreads-1].read_start+rd_dst[nreads-1].read_len > spot_len) in read_seg_from_meta() 144 for(i=0;i<nreads;i++) in read_seg_from_meta() 157 rslt -> elem_count = nreads; in read_seg_from_meta() [all …]
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H A D | spot-filter.c | 133 for (i = 0; i < nreads; ++i) { in check_quality() 174 , unsigned const nreads in check_dna() argument 181 for (i = 0; i < nreads; ++i) { in check_dna() 224 , unsigned const nreads in check_4na() argument 231 for (i = 0; i < nreads; ++i) { in check_4na() 267 , unsigned const nreads in check_x2na() argument 274 for (i = 0; i < nreads; ++i) { in check_x2na() 307 , unsigned const nreads in check_2na() argument 314 for (i = 0; i < nreads; ++i) { in check_2na() 485 for (i = 0; i < nreads; ++i) { in read_filter_array_to_bitset() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-pileup/ |
H A D | sam-unaligned.c | 164 uint32_t nreads; member 208 row->nreads = len; in read_seq_row() 273 if ( nreads > 1 ) in calculate_unaligned_sam_flags_db() 284 if ( read_idx == ( nreads - 1 ) ) in calculate_unaligned_sam_flags_db() 305 const uint32_t nreads, in get_mate_info() argument 315 if ( nreads < 2 ) in get_mate_info() 539 if ( rc == 0 && nreads != read_start_len ) in read_read_start() 552 if ( rc == 0 && nreads != read_len_len ) in read_read_len() 786 if ( nreads > 1 ) in dump_seq_prim_row_sam() 788 if ( read_idx == ( nreads - 1 ) ) in dump_seq_prim_row_sam() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/axf/ |
H A D | get-sam-flags.c | 54 uint32_t nreads, in get_sam_flags_impl() argument 78 if( nreads == 0 ) in get_sam_flags_impl() 109 if ( nreads > 1 ) in get_sam_flags_impl() 114 if ( rid[ 0 ] == nreads ) in get_sam_flags_impl() 153 uint32_t nreads = 0; in get_sam_flags_impl_v1() local 161 for ( i = 0, nreads = 0; i != argv[ 0 ].u.data.elem_count; ++i ) in get_sam_flags_impl_v1() 164 ++nreads; in get_sam_flags_impl_v1() 167 nreads = argv[ 0 ].u.data.elem_count; in get_sam_flags_impl_v1() 170 return get_sam_flags_impl( data, info, row_id, rslt, nreads, argc, argv ); in get_sam_flags_impl_v1() 178 uint32_t nreads = 1; in get_sam_flags_impl_v2() local [all …]
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/axf/ |
H A D | get-sam-flags.c | 54 uint32_t nreads, in get_sam_flags_impl() argument 78 if( nreads == 0 ) in get_sam_flags_impl() 109 if ( nreads > 1 ) in get_sam_flags_impl() 114 if ( rid[ 0 ] == nreads ) in get_sam_flags_impl() 153 uint32_t nreads = 0; in get_sam_flags_impl_v1() local 161 for ( i = 0, nreads = 0; i != argv[ 0 ].u.data.elem_count; ++i ) in get_sam_flags_impl_v1() 164 ++nreads; in get_sam_flags_impl_v1() 167 nreads = argv[ 0 ].u.data.elem_count; in get_sam_flags_impl_v1() 170 return get_sam_flags_impl( data, info, row_id, rslt, nreads, argc, argv ); in get_sam_flags_impl_v1() 178 uint32_t nreads = 1; in get_sam_flags_impl_v2() local [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-load/ |
H A D | sra-writer.c | 49 uint8_t nreads; member 62 uint8_t nreads; in SRAWriter_Make() local 67 if( (rc = Experiment_GetReadNumber(config->experiment, &nreads)) != 0 ) { in SRAWriter_Make() 75 obj->nreads = nreads; in SRAWriter_Make() 221 for (i = 0; i != self->nreads; ++i) { in SRAWriter_WriteDefaults() 229 for(i = 0; rc == 0 && i < self->nreads; i++) { in SRAWriter_WriteDefaults() 246 DEBUG_MSG (7, ("Default: %hu reads per spot, labels: '%s'\n", self->nreads, labels)); in SRAWriter_WriteDefaults() 247 for( i = 0; i < self->nreads; i++) { in SRAWriter_WriteDefaults() 259 … (rc = SRAWriter_WDflt(self, "NREADS", vdb_uint8_t, &self->nreads, sizeof(self->nreads))) != 0 || in SRAWriter_WriteDefaults() 307 for (i = 0; i < self->nreads; i++) { in SRAWriter_WriteSpotSegment() [all …]
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H A D | writer-absolid.c | 101 uint8_t nreads; member 125 uint8_t nreads; in SRAWriteAbsolid_Make() local 140 if( nreads > ABSOLID_FMT_MAX_NUM_READS ) { in SRAWriteAbsolid_Make() 183 if( nreads > 1 ) { in SRAWriteAbsolid_Make() 189 self->nreads = nreads; in SRAWriteAbsolid_Make() 229 uint32_t nreads; member 251 assert(nreads != 0); in AbsolidSpot_Init() 359 if( nreads == 0 || nreads > cself->nreads ) { in SRAWriteAbsolid_Write() 367 if( cself->nreads == 1 ) { in SRAWriteAbsolid_Write() 369 } else if( cself->nreads == 2 ) { in SRAWriteAbsolid_Write() [all …]
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H A D | writer-illumina.c | 173 if( spot->nreads == 0 ) { in IlluminaSpot_Add() 178 for(k = 0; k < spot->nreads; k++) { in IlluminaSpot_Add() 184 k = spot->nreads + 1; in IlluminaSpot_Add() 192 if( rc == 0 && k >= spot->nreads ) { in IlluminaSpot_Add() 206 uint8_t nreads; member 233 uint8_t nreads; in SRAWriterIllumina_Make() local 264 self->nreads = nreads; in SRAWriterIllumina_Make() 275 --nreads; in SRAWriterIllumina_Make() 303 if( nreads == 0 ) { in SRAWriterIllumina_Make() 327 } while( rc == 0 && nreads > 0 ); in SRAWriterIllumina_Make() [all …]
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H A D | srf-absolid.c | 59 uint8_t nreads; member 91 self->region.nreads = region_count / 2; in fe_new_region() 92 DEBUG_MSG(3, ("REGION: %u -> %u reads\n", region_count, self->region.nreads)); in fe_new_region() 93 if( self->region.nreads <= 0 || self->region.nreads > ABSOLID_FMT_MAX_NUM_READS ) { in fe_new_region() 97 for(i = 0; rc == 0 && i < self->region.nreads ; i++ ) { in fe_new_region() 211 if( fe->region.nreads == 0 ) { in parse_v1_read() 244 for(i = 1; i < fe->region.nreads; i++) { in parse_v1_read() 258 for(i = 0; rc == 0 && i < fe->region.nreads; i++) { in parse_v1_read() 287 for(i = 0; rc == 0 && i < fe->region.nreads; i++) { in parse_v1_read() 358 if( fe->region.nreads <= 0 || fe->region.nreads > ABSOLID_FMT_MAX_NUM_READS ) { in parse_v1_read() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/loader/ |
H A D | sequence-writer.c | 71 uint8_t nreads = rec->numreads; in SequenceWriteRecord() local 103 alcnt = (uint8_t *)&readLen[nreads]; in SequenceWriteRecord() 108 mask = (bool *)&readFilter[nreads]; in SequenceWriteRecord() 115 for (i = 0; i != nreads; ++i) { in SequenceWriteRecord() 152 data.nreads = nreads; in SequenceWriteRecord() 155 data.read_type.elements = nreads; in SequenceWriteRecord() 158 data.read_start.elements = nreads; in SequenceWriteRecord() 161 data.read_len.elements = nreads; in SequenceWriteRecord() 169 data.cskey.elements = nreads; in SequenceWriteRecord() 172 data.read_filter.elements = nreads; in SequenceWriteRecord() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/test/loader/ |
H A D | sequence-writer.c | 71 uint8_t nreads = rec->numreads; in SequenceWriteRecord() local 103 alcnt = (uint8_t *)&readLen[nreads]; in SequenceWriteRecord() 108 mask = (bool *)&readFilter[nreads]; in SequenceWriteRecord() 115 for (i = 0; i != nreads; ++i) { in SequenceWriteRecord() 152 data.nreads = nreads; in SequenceWriteRecord() 155 data.read_type.elements = nreads; in SequenceWriteRecord() 158 data.read_start.elements = nreads; in SequenceWriteRecord() 161 data.read_len.elements = nreads; in SequenceWriteRecord() 169 data.cskey.elements = nreads; in SequenceWriteRecord() 172 data.read_filter.elements = nreads; in SequenceWriteRecord() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/fastq-loader/ |
H A D | sequence-writer.c | 76 uint8_t nreads = rec->numreads; in SequenceWriteRecord() local 108 alcnt = (uint8_t *)&readLen[nreads]; in SequenceWriteRecord() 113 mask = (bool *)&readFilter[nreads]; in SequenceWriteRecord() 120 for (i = 0; i != nreads; ++i) { in SequenceWriteRecord() 157 data.nreads = nreads; in SequenceWriteRecord() 160 data.read_type.elements = nreads; in SequenceWriteRecord() 163 data.read_start.elements = nreads; in SequenceWriteRecord() 166 data.read_len.elements = nreads; in SequenceWriteRecord() 174 data.cskey.elements = nreads; in SequenceWriteRecord() 177 data.read_filter.elements = nreads; in SequenceWriteRecord() [all …]
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/loader/ |
H A D | sequence-writer.c | 71 uint8_t nreads = rec->numreads; in SequenceWriteRecord() local 103 alcnt = (uint8_t *)&readLen[nreads]; in SequenceWriteRecord() 108 mask = (bool *)&readFilter[nreads]; in SequenceWriteRecord() 115 for (i = 0; i != nreads; ++i) { in SequenceWriteRecord() 152 data.nreads = nreads; in SequenceWriteRecord() 155 data.read_type.elements = nreads; in SequenceWriteRecord() 158 data.read_start.elements = nreads; in SequenceWriteRecord() 161 data.read_len.elements = nreads; in SequenceWriteRecord() 169 data.cskey.elements = nreads; in SequenceWriteRecord() 172 data.read_filter.elements = nreads; in SequenceWriteRecord() [all …]
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/test/loader/ |
H A D | sequence-writer.c | 71 uint8_t nreads = rec->numreads; in SequenceWriteRecord() local 103 alcnt = (uint8_t *)&readLen[nreads]; in SequenceWriteRecord() 108 mask = (bool *)&readFilter[nreads]; in SequenceWriteRecord() 115 for (i = 0; i != nreads; ++i) { in SequenceWriteRecord() 152 data.nreads = nreads; in SequenceWriteRecord() 155 data.read_type.elements = nreads; in SequenceWriteRecord() 158 data.read_start.elements = nreads; in SequenceWriteRecord() 161 data.read_len.elements = nreads; in SequenceWriteRecord() 169 data.cskey.elements = nreads; in SequenceWriteRecord() 172 data.read_filter.elements = nreads; in SequenceWriteRecord() [all …]
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/dports/biology/star/STAR-2.7.9a/source/ |
H A D | SoloFeature_redistributeReadsByCB.cpp | 27 uint64 nreads=0; in redistributeReadsByCB() local 31 nreads += readFeatSum->cbReadCount[indCB[icb]]; in redistributeReadsByCB() 32 if (nreads>=nReadRecBin) { in redistributeReadsByCB() 35 redistrFilesNreads.push_back(nreads); in redistributeReadsByCB() 36 nreads=0; in redistributeReadsByCB() 39 if (nreads>0) { in redistributeReadsByCB() 41 redistrFilesNreads.push_back(nreads); in redistributeReadsByCB()
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/dports/devel/p5-Cache-FastMmap/Cache-FastMmap-1.57/t/ |
H A D | 14.t | 28 my ($nreads, $nreadhits) = $FC->get_statistics(); 30 cmp_ok( $nreads, '==', 102 ); 33 ($nreads, $nreadhits) = $FC->get_statistics(1); 35 cmp_ok( $nreads, '==', 102 ); 38 ($nreads, $nreadhits) = $FC->get_statistics(1); 40 cmp_ok( $nreads, '==', 0 );
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/test/ |
H A D | test_view.c | 44 int nreads; member 128 if (opts->nreads && --opts->nreads == 0) in sam_loop() 149 if (opts->nreads && --opts->nreads == 0) in sam_loop() 165 if (opts->nreads && --opts->nreads == 0) in sam_loop() 233 if (opts->nreads && --opts->nreads == 0) in vcf_loop() 254 if (opts->nreads && --opts->nreads == 0) in vcf_loop() 289 opts.nreads = 0; in main() 310 case 'N': opts.nreads = atoi(optarg); break; in main()
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/dports/biology/htslib/htslib-1.14/test/ |
H A D | test_view.c | 44 int nreads; member 130 if (opts->nreads && --opts->nreads == 0) in sam_loop() 151 if (opts->nreads && --opts->nreads == 0) in sam_loop() 167 if (opts->nreads && --opts->nreads == 0) in sam_loop() 235 if (opts->nreads && --opts->nreads == 0) in vcf_loop() 256 if (opts->nreads && --opts->nreads == 0) in vcf_loop() 291 opts.nreads = 0; in main() 314 case 'N': opts.nreads = atoi(optarg); break; in main()
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/dports/biology/bowtie2/bowtie2-2.4.4/example/reads/ |
H A D | simulate.pl | 45 my $nreads = undef; # # reads 57 "nreads=i" => \$nreads, 102 $nreads = $nreads || 10000; # number of reads/end to generate 111 $nreads = 6000; 193 @readlens = ($rdlen_exact) x ($nreads * ($paired ? 2 : 1)); 195 @readlens = random_exponential($nreads * ($paired ? 2 : 1), $rdlen_av); 201 @fraglens = random_normal($nreads, $frag_av, $frag_sd);
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