/dports/biology/star/STAR-2.7.9a/source/ |
H A D | GTF_transcriptGeneSJ.cpp | 37 for (uint64 iex=0; iex<exonN; iex++) { in transcriptGeneSJ() local 38 exgeLoci[GTF_exgeExStart(iex)]=exonLoci[iex][exS]; in transcriptGeneSJ() 39 exgeLoci[GTF_exgeExEnd(iex)]=exonLoci[iex][exE]; in transcriptGeneSJ() 41 exgeLoci[GTF_exgeGeID(iex)]=exonLoci[iex][exG]; in transcriptGeneSJ() 42 exgeLoci[GTF_exgeTrID(iex)]=exonLoci[iex][exT]; in transcriptGeneSJ() 49 for (uint64 iex=0; iex<exonN; iex++) { in transcriptGeneSJ() local 69 for (uint64 iex=0; iex<=exonN; iex++) { in transcriptGeneSJ() local 78 extrLoci[GTF_extrTrID(iex)]=exonLoci[iex][exT]; in transcriptGeneSJ() 81 extrLoci[GTF_extrGeID(iex)]=exonLoci[iex][exG]; in transcriptGeneSJ() 96 for (uint64 iex=0;iex<=exonN; iex++) { in transcriptGeneSJ() local [all …]
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H A D | Transcriptome_quantAlign.cpp | 44 for (uint32 iex=0; iex<aT.nExons; iex++) { in alignToTranscript() local 45 aT.exons[iex][EX_R]=aG.Lread-(aT.exons[iex][EX_R]+aT.exons[iex][EX_L]); in alignToTranscript() 46 aT.exons[iex][EX_G]=trlength-(aT.exons[iex][EX_G]+aT.exons[iex][EX_L]); in alignToTranscript() 48 for (uint32 iex=0; iex<aT.nExons/2; iex++) { in alignToTranscript() local 49 swap(aT.exons[iex][EX_R],aT.exons[aT.nExons-1-iex][EX_R]); in alignToTranscript() 50 swap(aT.exons[iex][EX_G],aT.exons[aT.nExons-1-iex][EX_G]); in alignToTranscript() 51 swap(aT.exons[iex][EX_L],aT.exons[aT.nExons-1-iex][EX_L]); in alignToTranscript() 52 swap(aT.exons[iex][EX_iFrag],aT.exons[aT.nExons-1-iex][EX_iFrag]); in alignToTranscript() 54 for (uint32 iex=0; iex<(aT.nExons-1)/2; iex++) { in alignToTranscript() local 55 swap(aT.canonSJ[iex],aT.canonSJ[aT.nExons-2-iex]); in alignToTranscript() [all …]
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H A D | Transcript_alignScore.cpp | 13 for (uint iex=0;iex<nExons;iex++) { in alignScore() local 14 for (uint ii=0;ii<exons[iex][EX_L];ii++) { in alignScore() 15 char r1=R[ii+exons[iex][EX_R]]; in alignScore() 16 char g1=G[ii+exons[iex][EX_G]]; in alignScore() 27 for (uint iex=0;iex<nExons-1;iex++) {//score junctions in alignScore() local 28 if (sjAnnot[iex]==1) { in alignScore() 31 switch (canonSJ[iex]) { in alignScore() 35 …maxScore += (exons[iex+1][EX_R]-exons[iex][EX_R]-exons[iex][EX_L])*P.scoreInsBase + P.scoreInsOpen; in alignScore() 38 …maxScore += (exons[iex+1][EX_G]-exons[iex][EX_G]-exons[iex][EX_L])*P.scoreDelBase + P.scoreDelOpen; in alignScore()
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H A D | ReadAlign_peOverlapMergeMap.cpp | 186 for (uint iex=0; iex<t.nExons; iex++) {//cycle through the exons in peOverlapSEtoPE() local 187 …if (t.exons[iex][EX_R] >= mEnd[imate] || t.exons[iex][EX_R]+t.exons[iex][EX_L] <= mSta[imate]) {//… in peOverlapSEtoPE() 193 if (iex<t.nExons-1) { in peOverlapSEtoPE() 196 sjStr[nExons]=t.sjStr[iex]; in peOverlapSEtoPE() 213 exons[nExons][EX_L]-=t.exons[iex][EX_R]+t.exons[iex][EX_L]-mEnd[imate]; in peOverlapSEtoPE() 244 for (uint iex=0;iex<nExons;iex++) {//caclulate total mapped length in peOverlapSEtoPE() local 245 rLength += exons[iex][EX_L]; in peOverlapSEtoPE() 323 for (uint iex=0; iex<tempTrChim[ii].nExons; iex++) { in peOverlapChimericSEtoPE() local 326 segEx[ii]=iex; in peOverlapChimericSEtoPE() 343 for (uint iex=0; iex<tempTrChim[i1].nExons; iex++) { in peOverlapChimericSEtoPE() local [all …]
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H A D | stitchWindowAligns.cpp | 114 for (uint iex=0;iex<trA.nExons-1;iex++) { in stitchWindowAligns() local 140 for (uint iex=0;iex<trA.nExons-1;iex++) { in stitchWindowAligns() local 144 for (uint iex=0;iex<trA.nExons-1;iex++) { in stitchWindowAligns() local 145 if (trA.canonSJ[iex]==0 && trA.sjAnnot[iex]==0) return; in stitchWindowAligns() 156 for (uint iex=0;iex<trA.nExons;iex++) {// in stitchWindowAligns() local 170 for (uint iex=0;iex<trA.nExons-1;iex++) { in stitchWindowAligns() local 171 if (trA.canonSJ[iex]>=0 && trA.sjAnnot[iex]==0) { in stitchWindowAligns() 172 uint jS=trA.exons[iex][EX_G]+trA.exons[iex][EX_L]; in stitchWindowAligns() 182 for (uint iex=0;iex<trA.nExons-1;iex++) {//find the first exon of the second mate in stitchWindowAligns() local 184 iexM2=iex+1; in stitchWindowAligns() [all …]
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H A D | ReadAlign_outputTranscriptSJ.cpp | 14 for (uint iex=0;iex<trOut.nExons-1;iex++) {//record all junctions in outputTranscriptSJ() local 15 if (trOut.canonSJ[iex]>=0) {//only record junctions, not indels or mate gap in outputTranscriptSJ() 17 … *chunkOutSJ->oneSJ.start=trOut.exons[iex][EX_G]+trOut.exons[iex][EX_L]; //start of the intron in outputTranscriptSJ() 18 *chunkOutSJ->oneSJ.gap=trOut.exons[iex+1][EX_G]-*chunkOutSJ->oneSJ.start; in outputTranscriptSJ() 23 …hunkOutSJ->oneSJ.overhangLeft = min ( (uint32) trOut.exons[iex][EX_L],(uint32) trOut.exons[iex+1][… in outputTranscriptSJ() 42 *chunkOutSJ->oneSJ.motif=trOut.canonSJ[iex]; in outputTranscriptSJ() 43 … *chunkOutSJ->oneSJ.strand=(char) (trOut.canonSJ[iex]==0 ? 0 : (trOut.canonSJ[iex]+1)%2+1); in outputTranscriptSJ() 44 *chunkOutSJ->oneSJ.annot=trOut.sjAnnot[iex]; in outputTranscriptSJ()
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/dports/lang/elixir-devel/elixir-1.13.1/lib/elixir/lib/ |
H A D | integer.ex | 27 iex> Integer.is_odd(5) 30 iex> Integer.is_odd(6) 33 iex> Integer.is_odd(-5) 36 iex> Integer.is_odd(0) 52 iex> Integer.is_even(10) 55 iex> Integer.is_even(5) 61 iex> Integer.is_even(0) 78 iex> Integer.pow(2, 0) 80 iex> Integer.pow(2, 1) 89 iex> Integer.pow(3, 4) [all …]
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H A D | bitwise.ex | 11 iex> use Bitwise 26 iex> 1 &&& 1 34 iex> odd? = fn 38 iex> odd?.(1) 70 iex> bnot(2) 92 iex> ~~~2 131 iex> 9 &&& 3 167 iex> 9 ||| 3 234 iex> 1 <<< 2 237 iex> 1 <<< -2 [all …]
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/dports/lang/elixir/elixir-1.12.3/lib/elixir/lib/ |
H A D | integer.ex | 27 iex> Integer.is_odd(5) 30 iex> Integer.is_odd(6) 33 iex> Integer.is_odd(-5) 36 iex> Integer.is_odd(0) 52 iex> Integer.is_even(10) 55 iex> Integer.is_even(5) 61 iex> Integer.is_even(0) 78 iex> Integer.pow(2, 0) 80 iex> Integer.pow(2, 1) 89 iex> Integer.pow(3, 4) [all …]
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H A D | bitwise.ex | 11 iex> use Bitwise 26 iex> 1 &&& 1 34 iex> odd? = fn 38 iex> odd?.(1) 70 iex> bnot(2) 92 iex> ~~~2 131 iex> 9 &&& 3 167 iex> 9 ||| 3 234 iex> 1 <<< 2 237 iex> 1 <<< -2 [all …]
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/dports/devel/elixir-smppex/smppex-2.2.9/lib/smppex/ |
H A D | pdu.ex | 41 iex(1)> SMPPEX.Pdu.new(1) 80 iex(1)> pdu = SMPPEX.Pdu.new(1) 103 iex(1)> pdu = SMPPEX.Pdu.new(1) 252 iex(1)> pdu = SMPPEX.Pdu.new(4) 366 iex(1)> pdu = SMPPEX.Pdu.new(4) 367 iex(2)> SMPPEX.Pdu.resp?(pdu) 370 iex(4)> SMPPEX.Pdu.resp?(pdu) 405 iex(2)> SMPPEX.Pdu.bind?(pdu) 408 iex(4)> SMPPEX.Pdu.bind?(pdu) 466 iex(2)> SMPPEX.Pdu.source(pdu) [all …]
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/dports/shells/fish/fish-3.3.1/share/completions/ |
H A D | iex.fish | 1 complete -f -c iex -s v -d "Prints version and exit" 2 complete -f -c iex -s e -d "Evaluates the given command" 3 complete -c iex -s r -d "Requires the given files/patterns" 4 complete -c iex -s S -d "Finds and executes the given script" 5 complete -c iex -s pr -d "Requires the given files/patterns in parallel" 6 complete -c iex -s pa -d "Prepends the given path to Erlang code path" 7 complete -c iex -s pz -d "Appends the given path to Erlang code path" 8 complete -c iex -l app -d "Start the given app and its dependencies" 9 complete -f -c iex -l erl -d "Switches to be passed down to erlang" 13 complete -f -c iex -l hidden -d "Makes a hidden node" [all …]
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/dports/lang/elixir/elixir-1.12.3/lib/ex_unit/test/ex_unit/ |
H A D | doc_test_test.exs | 19 iex> one() 21 iex> one() + 1 41 iex> a = 1 44 iex> a + b 88 iex> 1 + "" 90 iex> 2 + "" 99 iex> one() 107 iex> two() 118 iex> 1 + 1 123 iex> one() [all …]
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/dports/devel/elixir-inflex/inflex-1.4.1/ |
H A D | README.md | 44 Here are some basic examples from `iex`: 48 iex(1)> Inflex.singularize("dogs") 51 iex(2)> Inflex.pluralize("dog") 54 iex(3)> Inflex.singularize("people") 57 iex(4)> Inflex.pluralize("person") 67 iex(1)> Inflex.pluralize("piano") 70 iex(2)> Inflex.pluralize("hero") 73 iex(3)> Inflex.pluralize("butterfly") 76 iex(4)> Inflex.pluralize("monkey") 84 iex(1)> Inflex.inflect("child", 1) [all …]
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/dports/lang/elixir-devel/elixir-1.13.1/lib/ex_unit/test/ex_unit/ |
H A D | doc_test_test.exs | 19 iex> one() 21 iex> one() + 1 41 iex> a = 1 44 iex> a + b 96 iex> 1 + "" 98 iex> 2 + "" 107 iex> one() 115 iex> two() 126 iex> 1 + 1 131 iex> one() [all …]
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/dports/devel/elixir-calendar/calendar-0.17.4/lib/calendar/ |
H A D | date.ex | 26 iex> from_erl({2014,12,27}) 29 iex> from_erl({2014,99,99}) 44 iex> from_erl! {2014,12,27} 478 iex> {2015, 7, 6} |> monday? 480 iex> {2015, 7, 7} |> monday? 528 iex> {2015, 7, 7} |> friday? 552 iex> {2015, 7, 7} |> sunday? 561 iex> from_ordinal(2015, 1) 585 iex> from_ordinal!(2015, 1) 602 iex> {2015, 7, 12} |> to_s [all …]
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/dports/devel/elixir-decimal/decimal-1.4.1/ |
H A D | README.md | 22 iex> alias Decimal, as: D 24 iex> D.add(D.new(6), D.new(7)) 26 iex> D.div(D.new(1), D.new(3)) 48 iex> D.get_context 58 iex> Decimal.get_context 84 iex> D.div(D.new(31), D.new(2)) 100 iex> D.get_context.traps 102 iex> D.get_context.flags 106 iex> D.get_context.flags 126 iex> D.get_context.traps [all …]
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/dports/devel/elixir-csv/csv-2.1.1/lib/ |
H A D | csv.ex | 51 iex> |> File.stream! 52 iex> |> CSV.decode 53 iex> |> Enum.take(2) 60 iex> |> File.stream! 61 iex> |> CSV.decode 62 iex> |> Enum.take(2) 78 iex> |> Enum.take(2) 90 iex> |> Enum.take(2) 140 iex> |> CSV.decode! 149 iex> |> CSV.decode! [all …]
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/mcscf/detci_sym/ |
H A D | detci_spin.F | 180 do iex=1,nexa 181 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra) 182 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra) 188 do iex=1,nexb 285 do iex=1,nexa 286 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra) 287 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra) 299 do iex=1,nexb 300 iib = exb(5,iex,istrb) 301 jjb = exb(6,iex,istrb) [all …]
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/mcscf/detci_sym/ |
H A D | detci_spin.F | 180 do iex=1,nexa 181 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra) 182 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra) 188 do iex=1,nexb 285 do iex=1,nexa 286 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra) 287 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra) 299 do iex=1,nexb 300 iib = exb(5,iex,istrb) 301 jjb = exb(6,iex,istrb) [all …]
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/dports/science/nwchem-data/nwchem-7.0.2-release/src/mcscf/detci/ |
H A D | detci_spin.F | 180 do iex=1,nexa 181 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra) 182 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra) 188 do iex=1,nexb 287 do iex=1,nexa 288 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra) 289 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra) 301 do iex=1,nexb 302 iib = exb(5,iex,istrb) 303 jjb = exb(6,iex,istrb) [all …]
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/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/mcscf/detci/ |
H A D | detci_spin.F | 180 do iex=1,nexa 181 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra) 182 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra) 188 do iex=1,nexb 287 do iex=1,nexa 288 eij(exa(6,iex,istra),exa(5,iex,istra)) = exa(1,iex,istra) 289 pij(exa(6,iex,istra),exa(5,iex,istra)) = exa(4,iex,istra) 301 do iex=1,nexb 302 iib = exb(5,iex,istrb) 303 jjb = exb(6,iex,istrb) [all …]
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/dports/lang/elixir/elixir-1.12.3/lib/elixir/lib/calendar/ |
H A D | time.ex | 9 iex> ~T[23:00:07.001] 15 iex> time = ~T[23:00:07.001] 16 iex> time.hour 18 iex> time.microsecond 56 iex> time = Time.utc_now() 57 iex> time.hour >= 0 91 iex> Time.new(0, 0, 0, 0) 93 iex> Time.new(23, 59, 59, 999_999) 96 iex> Time.new(24, 59, 59, 999_999) 98 iex> Time.new(23, 60, 59, 999_999) [all …]
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/dports/lang/elixir-devel/elixir-1.13.1/lib/elixir/lib/calendar/ |
H A D | time.ex | 9 iex> ~T[23:00:07.001] 15 iex> time = ~T[23:00:07.001] 16 iex> time.hour 18 iex> time.microsecond 56 iex> time = Time.utc_now() 57 iex> time.hour >= 0 91 iex> Time.new(0, 0, 0, 0) 93 iex> Time.new(23, 59, 59, 999_999) 96 iex> Time.new(24, 59, 59, 999_999) 98 iex> Time.new(23, 60, 59, 999_999) [all …]
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/dports/astro/gpsman/gpsman-6.4.4.2/manual/html/info/ |
H A D | instupdate.tcl | 159 set iex "" 161 if { [catch {set iex [exec which gpsman]}] && \ 165 set iex $f 172 if { $iex == "" || [catch {set v [exec $iex show version]}] || \ 176 gets stdin iex 177 if { [file pathtype $iex] != "absolute" || \ 183 } elseif { $iex == "" } { 186 gets stdin iex 193 set isd [FindValues SRCDIR $iex] 218 set fiex $iex [all …]
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