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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/test/sraxf/
H A Dfix_read_seg-test.cpp22 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
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/test/sraxf/
H A Dfix_read_seg-test.cpp22 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
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/
H A Dsequence-writer.c80 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/sraxf/
H A Dread-seg-from-readn.c82 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()
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H A Dspot-filter.c133 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()
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H A Dfix_read_seg_impl.h38 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()
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/sraxf/
H A Dread-seg-from-readn.c82 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()
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H A Dspot-filter.c133 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-pileup/
H A Dsam-unaligned.c164 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/axf/
H A Dget-sam-flags.c54 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
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/axf/
H A Dget-sam-flags.c54 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
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-load/
H A Dsra-writer.c49 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()
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H A Dwriter-absolid.c101 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()
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H A Dwriter-illumina.c173 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()
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H A Dsrf-absolid.c59 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/loader/
H A Dsequence-writer.c71 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/test/loader/
H A Dsequence-writer.c71 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/fastq-loader/
H A Dsequence-writer.c76 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()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/loader/
H A Dsequence-writer.c71 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()
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/test/loader/
H A Dsequence-writer.c71 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()
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/dports/biology/star/STAR-2.7.9a/source/
H A DSoloFeature_redistributeReadsByCB.cpp27 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()
/dports/devel/p5-Cache-FastMmap/Cache-FastMmap-1.57/t/
H A D14.t28 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 );
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/test/
H A Dtest_view.c44 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()
/dports/biology/htslib/htslib-1.14/test/
H A Dtest_view.c44 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()
/dports/biology/bowtie2/bowtie2-2.4.4/example/reads/
H A Dsimulate.pl45 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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