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/dports/devel/rust-analyzer/rust-analyzer-2021-12-20/crates/text_edit/src/
H A Dlib.rs22 indels: Vec<Indel>, field
27 indels: Vec<Indel>, field
72 self.indels.len() in len()
76 self.indels.is_empty() in is_empty()
124 self.indels.extend(other.indels); in union()
152 self.indels.into_iter() in into_iter()
161 self.indels.iter() in into_iter()
167 self.indels.is_empty() in is_empty()
179 let mut indels = self.indels; in finish() localVariable
181 TextEdit { indels } in finish()
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/dports/lang/rust/rustc-1.58.1-src/src/tools/rust-analyzer/crates/text_edit/src/
H A Dlib.rs22 indels: Vec<Indel>, field
27 indels: Vec<Indel>, field
72 self.indels.len() in len()
76 self.indels.is_empty() in is_empty()
124 self.indels.extend(other.indels); in union()
152 self.indels.into_iter() in into_iter()
161 self.indels.iter() in into_iter()
167 self.indels.is_empty() in is_empty()
179 let mut indels = self.indels; in finish() localVariable
181 TextEdit { indels } in finish()
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/dports/biology/gatk/gatk-4.2.0.0/scripts/cnn_variant_wdl/
H A Dvcf_analysis.R139 indels <- subset(d, EVENTLENGTH != 0) globalVar
141 indels$QUALITY_BIN <- cut(indels[[score_key]], breaks=my_breaks, include.lowest=T, labels=F)
142 indels$QUALITY_BIN_RANGE <- cut(indels[[score_key]], breaks=my_breaks, include.lowest=T)
146 indels$QUALITY_LOD <- q_means[indels$QUALITY_BIN]
147 indels$TPR_PREDICTION <- exp(indels$QUALITY_LOD) / (1 + exp(indels$QUALITY_LOD))
148 x <- rowsum(indels$ONE, indels$QUALITY_BIN)
149 indels$BIN_SUM <- x[indels$QUALITY_BIN]
150 indels$TPR <- get_proportion(indels, num_bins, indels$TP, indels$QUALITY_BIN)
151 indels$ONEBP <- as.numeric(abs(indels$EVENTLENGTH)==1)
152 indels$PROPORTION_ONEBP <- get_proportion(indels, num_bins, indels$ONEBP, indels$QUALITY_BIN)
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H A Dvcf_analysis_no_truth.R126 indels <- subset(d, EVENTLENGTH != 0) globalVar
127 my_breaks <- ifelse(bin_by_quantile, quantile(indels[[score_key]], probs = seq(0, 1, 1.0/num_bins),…
128 indels$QUALITY_BIN <- cut(indels[[score_key]], breaks=my_breaks, include.lowest=T, labels=F)
129 indels$QUALITY_BIN_RANGE <- cut(indels[[score_key]], breaks=my_breaks, include.lowest=T)
130 mine <- lapply(strsplit(sapply(levels(indels$QUALITY_BIN_RANGE), function(x) substr(x, 2, nchar(x)-…
133 indels$QUALITY_LOD <- q_means[indels$QUALITY_BIN]
134 x <- rowsum(indels$ONE, indels$QUALITY_BIN)
135 indels$BIN_SUM <- x[indels$QUALITY_BIN]
136 indels$ONEBP <- as.numeric(abs(indels$EVENTLENGTH)==1)
137 indels$PROPORTION_ONEBP <- get_proportion(indels, num_bins, indels$ONEBP, indels$QUALITY_BIN)
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/dports/biology/gmap/gmap-2020-09-12/src/
H A Dindel.c64 Univcoord_T left, int indels, in Indel_resolve_middle_insertion() argument
83 assert(indels > 0); in Indel_resolve_middle_insertion()
152 Genome_fill_buffer_blocks(left+indels,querylength-indels,gbuffer); in Indel_resolve_middle_insertion()
154 plusp,want_lowest_coordinate_p,(unsigned long long) left,indels,(unsigned long long) left+indels); in Indel_resolve_middle_insertion()
156 printf("g2: %s\n",&(gbuffer[indels])); in Indel_resolve_middle_insertion()
382 Univcoord_T left, int indels, in Indel_resolve_middle_deletion() argument
401 assert(indels < 0); in Indel_resolve_middle_deletion()
669 Univcoord_T left, int indels, in Indel_resolve_middle_deletion_or_splice() argument
719 assert(indels < 0); in Indel_resolve_middle_deletion_or_splice()
729 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
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/dports/biology/py-cutadapt/cutadapt-3.3/tests/
H A Dtest_adapters.py136 indels=True,
154 indels=True,
274 adapter = adapter_class("ACGT", indels=False)
304 PrefixAdapter("GAAC", indels=False),
305 PrefixAdapter("TGCT", indels=False),
318 PrefixAdapter("GAAC", indels=False),
319 SuffixAdapter("TGCT", indels=False),
342 SuffixAdapter("GAAC", indels=False),
343 SuffixAdapter("TGCT", indels=False),
355 SuffixAdapter("GAAC", indels=False),
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H A Dtest_parser.py41 adapter_wildcards=False, indels=False)
54 assert not a.indels
143 adapter_wildcards=False, indels=False)
252 a = AdapterParser(max_errors=0.17, indels=False)._parse("ACG...TGT")
256 assert not a.front_adapter.indels
257 assert not a.back_adapter.indels
269 adapter_wildcards=False, indels=True)
284 adapter_wildcards=False, indels=True)
/dports/biology/vcflib/vcflib-1.0.2/smithwaterman/
H A DLeftAlign.cpp39 vector<IndelAllele> indels; in leftAlign() local
95 for (vector<IndelAllele>::iterator a = indels.begin(); a != indels.end(); ++a) cerr << *a << " "; in leftAlign()
104 for (vector<IndelAllele>::iterator id = indels.begin(); id != indels.end(); ++id) { in leftAlign()
201 if (indels.size() > 1) { in leftAlign()
203 for (vector<IndelAllele>::iterator id = (indels.begin() + 1); id != indels.end(); ++id) { in leftAlign()
302 if (!indels.empty()) { in leftAlign()
366 for (vector<IndelAllele>::iterator i = indels.begin(); i != indels.end(); ++i) { in leftAlign()
409 for (vector<IndelAllele>::iterator i = indels.begin(); i != indels.end(); ++i) { in leftAlign()
445 for (vector<IndelAllele>::iterator i = indels.begin(); i != indels.end(); ++i) { in leftAlign()
464 if (indels.size() > 1) { in leftAlign()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/smithwaterman/
H A DLeftAlign.cpp39 vector<IndelAllele> indels; in leftAlign() local
95 for (vector<IndelAllele>::iterator a = indels.begin(); a != indels.end(); ++a) cerr << *a << " "; in leftAlign()
104 for (vector<IndelAllele>::iterator id = indels.begin(); id != indels.end(); ++id) { in leftAlign()
201 if (indels.size() > 1) { in leftAlign()
203 for (vector<IndelAllele>::iterator id = (indels.begin() + 1); id != indels.end(); ++id) { in leftAlign()
302 if (!indels.empty()) { in leftAlign()
366 for (vector<IndelAllele>::iterator i = indels.begin(); i != indels.end(); ++i) { in leftAlign()
409 for (vector<IndelAllele>::iterator i = indels.begin(); i != indels.end(); ++i) { in leftAlign()
445 for (vector<IndelAllele>::iterator i = indels.begin(); i != indels.end(); ++i) { in leftAlign()
464 if (indels.size() > 1) { in leftAlign()
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/dports/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7/
H A DLeftAlign.cpp39 vector<IndelAllele> indels; in leftAlign() local
95 for (vector<IndelAllele>::iterator a = indels.begin(); a != indels.end(); ++a) cerr << *a << " "; in leftAlign()
104 for (vector<IndelAllele>::iterator id = indels.begin(); id != indels.end(); ++id) { in leftAlign()
201 if (indels.size() > 1) { in leftAlign()
203 for (vector<IndelAllele>::iterator id = (indels.begin() + 1); id != indels.end(); ++id) { in leftAlign()
302 if (!indels.empty()) { in leftAlign()
366 for (vector<IndelAllele>::iterator i = indels.begin(); i != indels.end(); ++i) { in leftAlign()
409 for (vector<IndelAllele>::iterator i = indels.begin(); i != indels.end(); ++i) { in leftAlign()
445 for (vector<IndelAllele>::iterator i = indels.begin(); i != indels.end(); ++i) { in leftAlign()
464 if (indels.size() > 1) { in leftAlign()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/dragstr/
H A DDragstrLocusCase.java50 return indels; in getIndels()
71 private final int indels; field in DragstrLocusCase
75 …strLocusCase create(final DragstrLocus locus, final int depth, final int indels, final int minMQ, … in create() argument
78 Utils.validateArg(indels >= 0, "the non-ref indel count must be 0 or positive"); in create()
81 return new DragstrLocusCase(locus, depth, indels, minMQ, nSup); in create()
87 this.indels = nonRef; in DragstrLocusCase()
/dports/biology/freebayes/freebayes-1.3.5/src/
H A DLeftAlign.cpp34 vector<FBIndelAllele> indels; in leftAlign() local
91 if (indels.empty()) { return false; } in leftAlign()
97 vector<FBIndelAllele>::iterator previous = indels.begin(); in leftAlign()
98 for (vector<FBIndelAllele>::iterator id = indels.begin(); id != indels.end(); ++id) { in leftAlign()
131 && (id == indels.begin() in leftAlign()
166 && (id == indels.begin() in leftAlign()
184 if (indels.size() > 1) { in leftAlign()
185 previous = indels.begin(); in leftAlign()
186 for (vector<FBIndelAllele>::iterator id = (indels.begin() + 1); id != indels.end(); ++id) { in leftAlign()
252 vector<FBIndelAllele>::iterator id = indels.begin(); in leftAlign()
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/dports/biology/vcf-split/vcf-split-0.1.3-3-g19713a4/Bench/
H A Dbcf-bench9 time bcftools view --genotype het --exclude-types indels --samples "$samples" \
15 time bcftools view --exclude-types indels \
21 time bcftools view --min-ac 2 --exclude-types indels \
27 time bcftools view --exclude-types indels --genotype het \
30 time bcftools view --min-ac 2 --exclude-types indels --genotype het \
/dports/biology/samtools/samtools-1.14/test/mpileup/
H A Dmpileup.reg25 INIT x $samtools view -S -b indels.sam > indels.bam
26 INIT x $samtools view -S -C indels.sam > indels.cram
118 P 53.out $samtools mpileup -e 1 -u -x -f mpileup.ref.fa indels.$fmt|$filter|$awk '/INDEL/'
119 P 54.out $samtools mpileup -e 10 -u -x -f mpileup.ref.fa indels.$fmt|$filter|$awk '/INDEL/'
120 P 55.out $samtools mpileup -h 10 -u -x -f mpileup.ref.fa indels.$fmt|$filter|$awk '/INDEL/'
121 P 56.out $samtools mpileup -h 90 -u -x -f mpileup.ref.fa indels.$fmt|$filter|$awk '/INDEL/'
122 P 57.out $samtools mpileup -e 1 -o 10 -u -x -f mpileup.ref.fa indels.$fmt|$filter|$awk '/INDEL/'
123 P 58.out $samtools mpileup -e 1 -o 40 -u -x -f mpileup.ref.fa indels.$fmt|$filter|$awk '/INDEL/'
126 P 59.out $samtools mpileup -x -F 0.60 -u -f mpileup.ref.fa indels.$fmt|$filter|$awk '/INDEL/'
127 P 60.out $samtools mpileup -x -F 0.66 -u -f mpileup.ref.fa indels.$fmt|$filter|$awk '/INDEL/'
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/dports/biology/subread/subread-2.0.2-source/src/
H A Dgene-value-index.c346 *indels = offset; in match_indel_chro_to_front()
477 indels[level] = this_record -> len; in match_indel_table_to_front_in()
488 indels[xk]=0; in match_indel_table_to_front_in()
516 while(indels[xk]) in match_indel_table_to_front_in()
517 ret_indels += indels[xk++]; in match_indel_table_to_front_in()
520 if(indels[0]) in match_indel_table_to_front_in()
596 indels[level] = this_record -> len; in match_indel_table_to_back_in()
605 indels[xk]=0; in match_indel_table_to_back_in()
635 memcpy(best_indels, indels, sizeof(short)*10); in match_indel_table_to_back_in()
671 *indels = 0; in match_indel_chro_to_back()
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H A Dgene-value-index.h56 … read, gene_value_index_t * index, unsigned int pos, int test_len, int * indels, int * indel_point…
57 … read, gene_value_index_t * index, unsigned int pos, int test_len, int * indels, int * indel_point…
59 …ead, gene_value_index_t * index, unsigned int pos, int test_len, short * indels, short * indel_poi…
60 …ead, gene_value_index_t * index, unsigned int pos, int test_len, short * indels, short * indel_poi…
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/loader/
H A Dreference-writer.c84 self->coverage.elem_bits = self->mismatches.elem_bits = self->indels.elem_bits = 32; in ReferenceInit()
129 KDataBufferWhack(&self->indels); in Unsorted()
142 unsigned *const indel = (unsigned *)self->indels.base; in FlushBuffers()
187 data.indels += indel[offset + i]; in FlushBuffers()
284 uint32_t const indels, in ReferenceAddCoverage() argument
300 BAIL_ON_FAIL(KDataBufferResize(&self->indels, newBaseCount)); in ReferenceAddCoverage()
326 ((unsigned *)self->indels.base)[startBase] += indels; in ReferenceAddCoverage()
415 unsigned indels; in ReferenceRead() local
418 GetCounts(data, seqLen, &nmatch, &nmis, &indels); in ReferenceRead()
423 data->data.ref_len, nmis, indels, in ReferenceRead()
[all …]
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/loader/
H A Dreference-writer.c84 self->coverage.elem_bits = self->mismatches.elem_bits = self->indels.elem_bits = 32; in ReferenceInit()
129 KDataBufferWhack(&self->indels); in Unsorted()
142 unsigned *const indel = (unsigned *)self->indels.base; in FlushBuffers()
187 data.indels += indel[offset + i]; in FlushBuffers()
284 uint32_t const indels, in ReferenceAddCoverage() argument
300 BAIL_ON_FAIL(KDataBufferResize(&self->indels, newBaseCount)); in ReferenceAddCoverage()
326 ((unsigned *)self->indels.base)[startBase] += indels; in ReferenceAddCoverage()
415 unsigned indels; in ReferenceRead() local
418 GetCounts(data, seqLen, &nmatch, &nmis, &indels); in ReferenceRead()
423 data->data.ref_len, nmis, indels, in ReferenceRead()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dvariations.cpp15 TLiteInDels indels; in BEGIN_SCOPE() local
16 indels.reserve(sam_indels.size()); in BEGIN_SCOPE()
55 return indels; in BEGIN_SCOPE()
61 m_indels.reserve(indels.size()); in CLiteAlign()
62 ITERATE( TLiteInDels, indl, indels) { in CLiteAlign()
142 m_indels.reserve(indels.size()); in CLiteAlign()
143 ITERATE(TLiteInDels, indl, indels) { in CLiteAlign()
233 TLiteInDels indels; in AddAlignment() local
357 ITERATE(TLiteInDelsP, indl, indels) { in InsertDashesInBase()
360 if(indl != indels.begin()) { in InsertDashesInBase()
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H A Dgnomon_objmgr.cpp107 TInDels indels; in CAlignModel() local
252 indels.push_back(fs); in CAlignModel()
254 indels.insert(indels.begin(), fs); in CAlignModel()
261 …indels.insert(indels.begin(), CInDelInfo(nuc_cur_end-pos-genomic_ins+1, genomic_ins, CInDelInfo::e… in CAlignModel()
278 …indels.insert(indels.begin(), CInDelInfo(nuc_cur_end-pos-mismatch_len+1, mismatch_len, CInDelInfo:… in CAlignModel()
288 indels.back().SetStatus(indelstatus); in CAlignModel()
329 NON_CONST_ITERATE(TInDels, indl, indels) { in CAlignModel()
331 if(++indl_next == indels.end()) in CAlignModel()
339 indels.erase(indl_next); in CAlignModel()
344 indels.erase(indl_next); in CAlignModel()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seq/unit_test/mapper_test_data/
H A Dspliced.asn418 -- Trimming indels: mapping alignment
468 -- Trimming indels: original
493 -- Trimming indels: mapped
530 -- Trimming indels: original-2
555 -- Trimming indels: mapped-2
594 -- Trimming indels - 3: mapping source
607 -- Trimming indels - 3: mapping destination
620 -- Trimming indels - 3: original
652 -- Trimming indels - 3: mapped, original indels must be preserved
712 -- Trimming indels on minus strand: original
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/dports/biology/vsearch/vsearch-2.17.1/src/
H A Dalign.cc339 int64_t indels = 0; in nw_align() local
365 indels++; in nw_align()
372 indels++; in nw_align()
379 indels++; in nw_align()
391 indels++; in nw_align()
417 indels++; in nw_align()
431 indels++; in nw_align()
454 * nwindels = indels; in nw_align()
/dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/
H A Dreference-writer.c85 self->coverage.elem_bits = self->mismatches.elem_bits = self->indels.elem_bits = 32; in ReferenceInit()
130 KDataBufferWhack(&self->indels); in Unsorted()
145 unsigned *const indel = (unsigned *)self->indels.base; in FlushBuffers()
190 data.indels += indel[offset + i]; in FlushBuffers()
404 uint32_t const indels, in ReferenceAddCoverage() argument
420 BAIL_ON_FAIL(KDataBufferResize(&self->indels, newBaseCount)); in ReferenceAddCoverage()
446 ((unsigned *)self->indels.base)[startBase] += indels; in ReferenceAddCoverage()
518 unsigned indels = 0; in ReferenceRead() local
530 GetCounts(data, seqLen, &nmatch, &nmis, &indels); in ReferenceRead()
546 data->data.ref_len, nmis, indels, in ReferenceRead()
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/dports/biology/bcftools/bcftools-1.14/test/
H A Dcheck.chk9 # number of indels .. number of rows with an indel
25 SN 0 number of indels: 9
33 …of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consiste…
36 …of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consiste…
42 …of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
90 …hat the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and i…
/dports/biology/bio-mocha/bcftools-1.14/test/
H A Dcheck.chk9 # number of indels .. number of rows with an indel
25 SN 0 number of indels: 9
33 …of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consiste…
36 …of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consiste…
42 …of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
90 …hat the ref/het/hom counts include only SNPs, for indels see PSI. The rest include both SNPs and i…

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