/dports/biology/bbmap/bbmap/current/template/ |
H A D | A_Sample2.java | 74 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in A_Sample2() 81 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process() 108 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 148 private final FileFormat ffin1; field in A_Sample2
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H A D | A_SampleSummary.java | 74 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in A_SampleSummary() 81 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process() 94 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 145 private final FileFormat ffin1; field in A_SampleSummary
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H A D | A_SampleD.java | 83 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in A_SampleD() 89 maxReads, false, ffin1, null, Shared.USE_MPI, Shared.MPI_KEEP_ALL); in process() 116 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==crisD.paired()); in process() 157 private final FileFormat ffin1; field in A_SampleD
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H A D | A_Sample_Unpaired.java | 128 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in A_Sample_Unpaired() 135 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); in process() 141 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process() 166 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 237 private final FileFormat ffin1; field in A_Sample_Unpaired
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H A D | A_Sample.java | 107 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in A_Sample() 275 …ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1,… in makeCris() 279 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in makeCris() 290 if(pairedInput && out2==null && (in1!=null && !ffin1.samOrBam() && !ffout1.samOrBam())){ in makeCros() 311 assert(ffin1.samOrBam() || (r.mate!=null)==cris.paired()); in processInner() 441 private final FileFormat ffin1; field in A_Sample
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H A D | BBTool_ST.java | 162 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in BBTool_ST() 276 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in startup() 281 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in startup() 347 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner() 435 protected final FileFormat ffin1; field in BBTool_ST
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/dports/biology/bbmap/bbmap/current/prok/ |
H A D | FilterSilva.java | 133 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in FilterSilva() 142 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process() 148 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process() 173 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 249 private final FileFormat ffin1; field in FilterSilva
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/dports/biology/bbmap/bbmap/current/tax/ |
H A D | FilterByTaxa.java | 194 ffin1=FileFormat.testInput(in1, FileFormat.FASTA, extin, true, true); in FilterByTaxa() 214 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 219 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process() 226 if(cris.paired() && out2==null && (in1!=null && !ffin1.samOrBam() && !ffout1.samOrBam())){ in process() 282 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner() 415 private final FileFormat ffin1; field in FilterByTaxa
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H A D | PrintTaxonomy.java | 152 ffin1=FileFormat.testInput(in1, FileFormat.TEXT, null, true, false); in PrintTaxonomy() 184 if(ffin1!=null){ in process() 185 if(ffin1.fasta() || ffin1.fastq() || ffin1.samOrBam() || ffin1.scarf()){ in process() 188 processFile(new TextFile(ffin1), tsw); in process() 245 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in processReads() 535 private final FileFormat ffin1;
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H A D | SplitByTaxa.java | 194 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in SplitByTaxa() 211 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, null, null); in process() 216 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process() 262 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner() 363 private final FileFormat ffin1; field in SplitByTaxa
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/dports/biology/bbmap/bbmap/current/jgi/ |
H A D | IdentityMatrix.java | 89 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in IdentityMatrix() 162 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in load() 179 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in load() 233 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in run() 292 private final FileFormat ffin1; field in IdentityMatrix
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H A D | TetramerFrequencies.java | 101 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in TetramerFrequencies() 102 assert(ffin1!=null) : "No input file."; in TetramerFrequencies() 103 assert(ffin1.exists() && ffin1.canRead()) : "Cannot read input file "+in1+"."; in TetramerFrequencies() 135 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process() 146 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 522 private final FileFormat ffin1;
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H A D | PartitionReads.java | 226 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in PartitionReads() 229 …useSharedHeader=(ffin1.samOrBam() && ffout1!=null && ffout1.length>0 && ffout1[0]!=null && ffout1[… in PartitionReads() 242 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 247 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process() 299 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner() 410 private final FileFormat ffin1; field in PartitionReads
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H A D | KeepBestCopy.java | 134 ffin1=FileFormat.testInput(in1, FileFormat.FASTA, extin, true, true); in KeepBestCopy() 139 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, qfin1, null); in makeCris() 149 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process() 163 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 277 private final FileFormat ffin1; field in KeepBestCopy
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H A D | ReplaceHeaders.java | 201 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in ReplaceHeaders() 219 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in process() 224 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process() 243 if(cris.paired() && out2==null && (in1!=null && !ffin1.samOrBam() && !ffout1.samOrBam())){ in process() 300 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner() 435 private final FileFormat ffin1; field in ReplaceHeaders
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H A D | CutPrimers.java | 83 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in CutPrimers() 90 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process() 120 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 224 private final FileFormat ffin1; field in CutPrimers
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/dports/biology/bbmap/bbmap/current/driver/ |
H A D | ReduceSilva.java | 120 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in ReduceSilva() 144 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process() 149 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process() 217 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in processInner() 304 private final FileFormat ffin1; field in ReduceSilva
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H A D | FilterReadsByName.java | 233 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in FilterReadsByName() 236 if(ffin1!=null && ffout1!=null && ffin1.samOrBam() && ffout1.samOrBam()){ in FilterReadsByName() 254 …cris=ConcurrentReadInputStream.getReadInputStream(maxReads, useSharedHeader, ffin1, ffin2, qfin1, … in process() 260 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process() 293 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 425 private final FileFormat ffin1; field in FilterReadsByName
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H A D | PlotGC.java | 125 ffin1=FileFormat.testInput(in1, FileFormat.FASTA, extin, true, true); in PlotGC() 132 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, null, null); in process() 156 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 266 private final FileFormat ffin1; field in PlotGC
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/dports/biology/bbmap/bbmap/current/icecream/ |
H A D | IceCreamGrader.java | 115 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in IceCreamGrader() 122 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null); in process() 139 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 218 private final FileFormat ffin1; field in IceCreamGrader
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/dports/biology/bbmap/bbmap/current/sketch/ |
H A D | InvertKey.java | 142 ffin1=FileFormat.testInput(in1, FileFormat.FASTA, null, true, true); in InvertKey() 176 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, null, null); in process() 182 …if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpai… in process() 205 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 303 private final FileFormat ffin1; field in InvertKey
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/dports/biology/bbmap/bbmap/current/ml/ |
H A D | ProcessBBMergeHeaders.java | 72 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in ProcessBBMergeHeaders() 79 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, false, ffin1, null); in process() 101 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 251 private final FileFormat ffin1; field in ProcessBBMergeHeaders
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/dports/biology/bbmap/bbmap/current/var2/ |
H A D | CompareVCF.java | 120 ffin1=new FileFormat[in1.length]; in CompareVCF() 122 ffin1[i]=FileFormat.testInput(in1[i], FileFormat.VCF, null, true, true); in CompareVCF() 164 for(FileFormat ff : ffin1){ in union() 172 for(FileFormat ff : ffin1){ in intersection() 182 for(FileFormat ff : ffin1){ in difference() 282 private final FileFormat ffin1[]; field in CompareVCF
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/dports/biology/bbmap/bbmap/current/hiseq/ |
H A D | PlotFlowCell.java | 188 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true); in PlotFlowCell() 234 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in loadKmers() 259 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2, qfin1, qfin2); in fillTiles() 300 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in loadKmersInner() 368 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in fillTilesInner() 568 private final FileFormat ffin1; field in PlotFlowCell
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/dports/biology/bbmap/bbmap/current/jasper/ |
H A D | KmerPosition.java | 85 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true); in KmerPosition() 95 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, ffin2); in process() 110 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired()); in process() 234 private final FileFormat ffin1; field in KmerPosition
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