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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/
H A DReferenceBasesUnitTest.java63 final String bases2 = "AGC"; in testGetNMiddleBases() local
64 Assert.assertEquals(ReferenceBases.getNMiddleBases(bases2, 3), "AGC"); in testGetNMiddleBases()
65 Assert.assertEquals(ReferenceBases.getNMiddleBases(bases2, 1), "G"); in testGetNMiddleBases()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/
H A DKmerUnitTest.java116 final byte[] bases2 = "TGCATGCA".getBytes(); in testStringsTooFar()
118 final Kmer eq2 = new Kmer(bases2, 0, 3); in testStringsTooFar()
119 final int[] differingIndices = new int[bases2.length]; in testStringsTooFar()
120 final byte[] differingBases = new byte[bases2.length]; in testStringsTooFar()
/dports/biology/bbmap/bbmap/current/jgi/
H A DShred.java295 final byte[] bases2=KillSwitch.copyOfRange(bases, a, b); in processEvenly()
297 Read shred=new Read(bases2, quals2, name+"_"+a+"-"+(b-1), readsOut); in processEvenly()
312 final byte[] bases2=KillSwitch.copyOfRange(bases, i, limit); in processUnevenly()
314 Read shred=new Read(bases2, quals2, name+"_"+i+"-"+(limit-1), readsOut, r1.flags); in processUnevenly()
332 final byte[] bases2=KillSwitch.copyOfRange(bases, i, limit);
334 Read shred=new Read(bases2, quals2, name+"_"+i+"-"+(limit-1), readsOut);
H A DCalcUniqueness.java354 final byte[] bases2=(r2==null ? null : r2.bases); in process()
358 final int length2=(bases2==null ? 0 : bases2.length); in process()
394 final long kmer=toKmer(bases2, quals2, singleOffset, k); in process()
399 final long kmer=toKmer(bases2, quals2, randy.nextInt(length2-k2), k); in process()
411 final long kmer2=toKmer(bases2, quals2, PAIR_OFFSET, k); in process()
H A DFakeReads.java240 byte[] bases2=KillSwitch.copyOfRange(r.bases, r.length()-len, r.length()); in process()
241 AminoAcid.reverseComplementBasesInPlace(bases2); in process()
253 … Read b=new Read(bases2, qual2, identifier+r.numericID+spacer+"/2", r.numericID, Read.PAIRNUMMASK); in process()
H A DBBMask.java455 byte[] bases2=KillSwitch.copyOfRange(bases, lastBad+1, i); in splitFromBitsets()
457 Read r2=new Read(bases2, quals2, r.id+"_"+rnum, r.numericID, r.flags); in splitFromBitsets()
470 byte[] bases2=KillSwitch.copyOfRange(bases, lastBad+1, i); in splitFromBitsets()
472 Read r2=new Read(bases2, quals2, r.id+"_"+rnum, r.numericID, r.flags); in splitFromBitsets()
H A DBBMerge.java1520 final byte[] bases1=r1.bases, bases2=r2.bases, basesj=joined.bases;
1524 for(int i=0, j=lenj-bases2.length; i<bases2.length && j<lenj; i++, j++){//count errors
1525 if(j>=0 && bases2[i]!=basesj[j] && AminoAcid.isFullyDefined(basesj[j])){e2++;}
H A DDedupe.java4373 final byte[] bases1=r.bases, bases2=u.r.bases;
4385 byte b1=bases1[i], b2=bases2[i];
4393 for(int i=0, j=bases2.length-1; i<bases1.length; i++, j--){
4394 byte b1=bases1[i], b2=baseToComplementExtended[bases2[j]];
H A DDedupe2.java4274 final byte[] bases1=r.bases, bases2=u.r.bases;
4286 byte b1=bases1[i], b2=bases2[i];
4294 for(int i=0, j=bases2.length-1; i<bases1.length; i++, j--){
4295 byte b1=bases1[i], b2=baseToComplementExtended[bases2[j]];
H A DDedupeProtein.java3948 final byte[] bases1=r.bases, bases2=u.r.bases; in absorbMatch()
3959 byte b1=bases1[i], b2=bases2[i]; in absorbMatch()
/dports/biology/bbmap/bbmap/current/shared/
H A DTrimRead.java179 …assert(bases2==null || bases2.length>=minlen_ || bases1.length<minlen_) : bases1.length+", "+bases… in TrimRead()
180 r.bases=bases2; in TrimRead()
228 bases2=bases1; in trim()
231 bases2=KillSwitch.copyOfRange(bases1, trimLeft, bases1.length-trimRight); in trim()
820 public byte[] bases2;
H A DReadStats.java301 bases=(pairnum==0 ? ((TrimRead)obj).bases1 : ((TrimRead)obj).bases2); in addToQualityHistogram2()
/dports/biology/sra-tools/sra-tools-2.11.0/tools/fasterq-dump/
H A Djoin_results.h65 bool join_results_match2( struct join_results * self, const String * bases1, const String * bases2 …
H A Djoin_results.c530 bool join_results_match2( struct join_results * self, const String * bases1, const String * bases2 ) in join_results_match2() argument
533 if ( NULL != self && NULL != bases1 && NULL != bases2 && NULL != self -> buf2na ) in join_results_match2()
535 …res = ( match_Buf2NA( self -> buf2na, bases1 ) || match_Buf2NA( self -> buf2na, bases2 ) ); /* hel… in join_results_match2()
/dports/biology/bbmap/bbmap/current/align2/
H A DRandomReads3.java841 byte[] bases2=new byte[bases.length+len]; in addInsertion()
842 for(int i=0; i<index; i++){bases2[i]=bases[i];} in addInsertion()
844 for(int i=bases.length-1, j=bases2.length-1; i>=index; i--, j--){ in addInsertion()
849 bases2[j]=bases[i]; in addInsertion()
860 bases2[i]=b; in addInsertion()
865 return bases2; in addInsertion()
892 byte[] bases2=new byte[bases.length-len]; in addDeletion()
893 for(int i=0; i<index; i++){bases2[i]=bases[i];} in addDeletion()
894 for(int i=index; i<bases2.length; i++){ in addDeletion()
895 bases2[i]=bases[i+len]; in addDeletion()
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/pileup/
H A DReadPileupUnitTest.java316 final byte[] bases2 = Utils.repeatChars('C', readlength); in testSimplePileup()
323 … final GATKRead read2 = ArtificialReadUtils.createArtificialRead(header, bases2, quals2, cigar2); in testSimplePileup()
365 final byte[] bases2 = Utils.repeatChars('C', readlength); in testSimplePileupWithIndelsOffset()
372 … final GATKRead read2 = ArtificialReadUtils.createArtificialRead(header, bases2, quals2, cigar2); in testSimplePileupWithIndelsOffset()
423 final byte[] bases2 = Utils.repeatChars('C', readlength); in testSimplePileupWithOffset()
430 … final GATKRead read2 = ArtificialReadUtils.createArtificialRead(header, bases2, quals2, cigar2); in testSimplePileupWithOffset()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/locusiterator/
H A DLocusIteratorByStateUnitTest.java117 final byte[] bases2 = {'A','A','A','C','A','A','A','A','A','C'}; in testXandEQOperators()
125 r2.setBases(bases2); in testXandEQOperators()
130 r3.setBases(bases2); in testXandEQOperators()
135 r4.setBases(bases2); in testXandEQOperators()
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/primer3/src/primer3_core/
H A Ddpal.c188 const unsigned char *bases1, *bases2, *b1, *b2; local
197 bases2 = xlate_ambiguity_code(*c2);
198 if (!bases2) return 0;
201 for (b2 = bases2; *b2; b2++) {
/dports/biology/primer3/primer3-2.3.6/src/
H A Ddpal.c193 const unsigned char *bases1, *bases2, *b1, *b2; in dpal_set_ambiguity_code_matrix() local
202 bases2 = xlate_ambiguity_code(*c2); in dpal_set_ambiguity_code_matrix()
203 if (!bases2) return 0; in dpal_set_ambiguity_code_matrix()
206 for (b2 = bases2; *b2; b2++) { in dpal_set_ambiguity_code_matrix()
/dports/textproc/py-pygccxml/pygccxml-2.2.1/unittests/
H A Dcore_tester.py233 bases2 = set([id(hierarchy_info.related_class)
236 bases1 == bases2,
/dports/lang/racket/racket-8.3/share/pkgs/typed-racket-lib/typed-racket/infer/
H A Dintersect.rkt136 [(t1 (BaseUnion-bases: bases2))
137 (apply Un (for/list ([b (in-list bases2)])
/dports/biology/bbmap/bbmap/current/icecream/
H A DReformatPacBio.java646 final byte[] bases2=KillSwitch.copyOfRange(bases, a, b); in shred()
648 Read shred=new Read(bases2, quals2, name+"_"+a+"-"+(b-1), r.numericID); in shred()
/dports/math/giacxcas/giac-1.6.0/src/
H A Dsubst.cc2368 vecteur bases,bases2; in simplify() local
2423 bases2.push_back(identificateur(" simplify_pow"+print_INT_(p))); in simplify()
2434 vabs2[i]=symb_pow(bases2[p],lcms[p]/expo[i]); in simplify()
2436 vabs2.push_back(symb_pow(bases2[p],lcms[p])); in simplify()
2449 e=quotesubst(e,bases2,bases,contextptr); in simplify()
/dports/devel/riscv64-gcc/gcc-8.3.0/gcc/testsuite/
H A DChangeLog3742 * g++.dg/ext/bases2.C: Expect extra error diagnostics.
/dports/devel/aarch64-none-elf-gcc/gcc-8.4.0/gcc/testsuite/
H A DChangeLog6387 * g++.dg/ext/bases2.C: Expect extra error diagnostics.

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