/dports/databases/opentsdb/opentsdb-2.3.0/test/tools/ |
H A D | TestFsck.java | 164 final byte[] qual1 = { 0x00, 0x07 }; in noErrors() 169 storage.addColumn(ROW, qual1, val1); in noErrors() 180 final byte[] qual1 = { 0x00, 0x07 }; in noErrorsMultipleRows() 185 storage.addColumn(ROW, qual1, val1); in noErrorsMultipleRows() 226 final byte[] qual1 = { 0x00, 0x07 }; in noErrorsAnnotation() 233 storage.addColumn(ROW, qual1, val1); in noErrorsAnnotation() 297 final byte[] qual1 = { 0x00, 0x07 }; in noErrorsCompacted() 331 final byte[] qual1 = { 0x00, 0x07 }; in noErrorsCompactedMix() 375 storage.getColumn(ROW, qual1)); in singleValueCompacted() 1552 MockBase.concatByteArrays(qual1, val1, qual1, val1, qual2, val2)); in appendDupe() [all …]
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/dports/databases/opentsdb/opentsdb-2.3.0/test/core/ |
H A D | TestRowSeq.java | 77 final byte[] qual1 = { 0x00, 0x07 }; in setRow() 93 final byte[] qual1 = { 0x00, 0x07 }; in setRowSalted() 108 final byte[] qual1 = { 0x00, 0x07 }; in setRowAlreadySet() 125 final byte[] qual1 = { 0x00, 0x07 }; in addRowMergeLater() 156 final byte[] qual1 = { 0x00, 0x07 }; in addRowMergeLaterSalted() 190 final byte[] qual1 = { 0x00, 0x37 }; in addRowMergeEarlier() 221 final byte[] qual1 = { 0x00, 0x37 }; in addRowMergeEarlierSalted() 255 final byte[] qual1 = { 0x00, 0x07 }; in addRowMergeMiddle() 298 final byte[] qual1 = { 0x00, 0x07 }; in addRowMergeMiddleSalted() 345 final byte[] qual1 = { 0x00, 0x07 }; in addRowMergeDuplicateLater() [all …]
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H A D | TestCompactionQueue.java | 259 kvs.add(makekv(qual1, val1)); in twoCellRow() 303 kvs.add(makekv(qual1, val1)); in twoCellRowWAnnotation() 402 kvs.add(makekv(qual1, val1)); in twoCellRowMS() 424 kvs.add(makekv(qual1, val1)); in sortMsAndS() 452 kvs.add(makekv(qual1, val1)); in secondsOutOfOrder() 482 kvs.add(makekv(qual1, val1)); in msOutOfOrder() 509 kvs.add(makekv(qual1, val1)); in secondAndMs() 533 kvs.add(makekv(qual1, val1)); in secondAndMsWAnnotation() 558 kvs.add(makekv(qual1, val1)); in msSameAsSecond() 572 kvs.add(makekv(qual1, val1)); in msSameAsSecondFix() [all …]
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H A D | TestSpan.java | 79 final byte[] qual1 = { 0x00, 0x07 }; in addRow() 98 final byte[] qual1 = { 0x00, 0x07 }; in addRowSalted() 125 final byte[] qual1 = { 0x00, 0x07 }; in addRowBadKeyLength() 143 final byte[] qual1 = { 0x00, 0x07 }; in addRowMissMatchedMetric() 161 final byte[] qual1 = { 0x00, 0x07 }; in addRowMissMatchedTagk() 179 final byte[] qual1 = { 0x00, 0x07 }; in addRowMissMatchedTagv() 197 final byte[] qual1 = { 0x00, 0x07 }; in addRowOutOfOrder() 222 final byte[] qual1 = { 0x00, 0x07 }; in timestampNormalized() 291 final byte[] qual1 = { 0x00, 0x07 }; in iterateNormalizedMS() 389 final byte[] qual1 = { 0x00, 0x07 }; in lastTimestampInRow() [all …]
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H A D | TestInternal.java | 44 final byte[] qual1 = { 0x00, 0x07 }; in extractDataPointsFixQualifierFlags() 52 row.add(makekv(qual1, val1)); in extractDataPointsFixQualifierFlags() 68 final byte[] qual1 = { 0x00, 0x0F }; in extractDataPointsFixFloatingPointValue() 76 row.add(makekv(qual1, val1)); in extractDataPointsFixFloatingPointValue() 92 final byte[] qual1 = { 0x00, 0x0F }; in extractDataPointsFixFloatingPointValueCorrupt() 100 row.add(makekv(qual1, val1)); in extractDataPointsFixFloatingPointValueCorrupt() 109 final byte[] qual1 = { 0x00, 0x27 }; in extractDataPointsMixSecondsMs() 117 row.add(makekv(qual1, val1)); in extractDataPointsMixSecondsMs() 129 final byte[] qual1 = { 0x00, 0x07 }; in extractDataPointsWithNonDataColumns() 137 row.add(makekv(qual1, val1)); in extractDataPointsWithNonDataColumns() [all …]
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/dports/biology/bowtie/bowtie-1.3.1/scripts/ |
H A D | reconcile_alignments_pe.pl | 210 my $qual1 = $s1[5]; 218 $qual1 = reverse $qual1; 234 $hits_hash{$read_name}{qual1} = $fasta ? "" : $qual1; 255 my ($name1, $seq1, $qual1) = get_read($UN1); 281 $un_hash{$name}{qual1} = $qual1; 328 $max_hash{$name}{qual1} = $qual1; 347 my ($name1, $seq1, $qual1) = get_read($AL1); 369 $al_hash{$name}{qual1} = $qual1; 427 $un_hash{$name}{qual1} eq $qual1 || 441 $max_hash{$name}{qual1} eq $qual1 || [all …]
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H A D | fastq_to_tabbed.pl | 98 my $qual1 = <M1>; 99 chomp($qual1); 102 print "$name1\t$seq1\t$qual1\t$seq2\t$qual2\n" unless $shuffle; 103 push @output, "$name1\t$seq1\t$qual1\t$seq2\t$qual2\n" if $shuffle;
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/dports/databases/hbase/hbase-1.2.1/hbase-common/src/test/java/org/apache/hadoop/hbase/ |
H A D | TestCellComparator.java | 40 byte[] qual1 = Bytes.toBytes("qual1"); field in TestCellComparator 47 KeyValue kv1 = new KeyValue(row1, fam1, qual1, val); in testCompareCells() 48 KeyValue kv2 = new KeyValue(row2, fam1, qual1, val); in testCompareCells() 51 kv1 = new KeyValue(row1, fam2, qual1, val); in testCompareCells() 52 kv2 = new KeyValue(row1, fam1, qual1, val); in testCompareCells() 55 kv1 = new KeyValue(row1, fam1, qual1, 1l, val); in testCompareCells() 56 kv2 = new KeyValue(row1, fam1, qual1, 2l, val); in testCompareCells() 59 kv1 = new KeyValue(row1, fam1, qual1, 1l, Type.Put); in testCompareCells() 63 kv1 = new KeyValue(row1, fam1, qual1, 1l, Type.Put); in testCompareCells() 67 kv1 = new KeyValue(row1, fam1, qual1, 1l, Type.Put); in testCompareCells() [all …]
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/dports/biology/bedtools/bedtools2-2.30.0/src/bamToFastq/ |
H A D | bamToFastq.cpp | 116 string qual1, qual2; in WritePairs() local 132 qual1 = alignments[0].Qualities; in WritePairs() 137 reverseSequence(qual1); in WritePairs() 152 reverseSequence(qual1); in WritePairs() 188 reverseSequence(qual1); in WritePairs() 220 reverseSequence(qual1); in WritePairs() 244 *_fq1 << qual1 << endl; in WritePairs() 295 string qual1 = bam1.Qualities; in PairedFastqUseTags() local 298 reverseSequence(qual1); in PairedFastqUseTags() 311 *_fq1 << qual1 << endl; in PairedFastqUseTags() [all …]
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/dports/security/py-stix2/cti-python-stix2-2.1.0/stix2/equivalence/pattern/compare/ |
H A D | observation.py | 26 def repeats_cmp(qual1, qual2): argument 30 return generic_constant_cmp(qual1.times_to_repeat, qual2.times_to_repeat) 33 def within_cmp(qual1, qual2): argument 38 qual1.number_of_seconds, qual2.number_of_seconds, 42 def startstop_cmp(qual1, qual2): argument 48 (qual1.start_time, qual1.stop_time),
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/dports/databases/opentsdb/opentsdb-2.3.0/src/core/ |
H A D | ColumnDatapointIterator.java | 72 final byte qual1 = qualifier[1]; in checkForFixup() 73 if (Internal.floatingPointValueToFix(qual1, value)) { in checkForFixup() 74 value = Internal.fixFloatingPointValue(qual1, value); in checkForFixup() 77 final byte lenByte = Internal.fixQualifierFlags(qual1, value.length); in checkForFixup() 78 if (lenByte != qual1) { in checkForFixup()
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/dports/databases/hbase/hbase-1.2.1/hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/ |
H A D | TestAtomicOperation.java | 131 a.add(fam1, qual1, Bytes.toBytes(v1)); in testAppend() 135 a.add(fam1, qual1, Bytes.toBytes(v2)); in testAppend() 175 assertICV(row, fam1, qual1, expectedTotal); in testIncrementMultiThreads() 241 inc.addColumn(fam1, qual1, amount); in run() 286 a.add(fam1, qual1, val); in testAppendMultiThreads() 365 p.add(fam1, qual1, value1); in testRowMutationMultiThreads() 374 d.deleteColumns(fam1, qual1, ts); in testRowMutationMultiThreads() 458 p.add(fam1, qual1, value1); in testMultiRowMutationMultiThreads() 462 d.deleteColumns(fam1, qual1, ts); in testMultiRowMutationMultiThreads() 467 d.deleteColumns(fam1, qual1, ts); in testMultiRowMutationMultiThreads() [all …]
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H A D | TestParallelPut.java | 68 static final byte[] qual1 = Bytes.toBytes("qual1"); field in TestParallelPut 117 put.add(fam1, qual1, Bytes.toBytes(value)); in testPut() 120 assertGet(this.region, row, fam1, qual1, Bytes.toBytes(value)); in testPut() 217 put.add(fam1, qual1, value); in run() 223 assertGet(this.region, rowkey, fam1, qual1, value); in run()
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/dports/databases/hbase/hbase-1.2.1/hbase-server/src/test/java/org/apache/hadoop/hbase/io/encoding/ |
H A D | TestPrefixTree.java | 62 private final static byte[] qual1 = Bytes.toBytes("qf_1"); field in TestPrefixTree 88 put.addColumn(fam, qual1, Bytes.toBytes("c1-value")); in testHBASE11728() 91 put.addColumn(fam, qual1, Bytes.toBytes("c1-value")); in testHBASE11728() 177 .put(new Put(Bytes.toBytes("obj" + (2900 + i))).addColumn(fam, qual1, Bytes.toBytes(i))); 179 region.put(new Put(Bytes.toBytes("obj299")).addColumn(fam, qual1, Bytes.toBytes("whatever"))); 180 region.put(new Put(Bytes.toBytes("obj29")).addColumn(fam, qual1, Bytes.toBytes("whatever"))); 181 region.put(new Put(Bytes.toBytes("obj2")).addColumn(fam, qual1, Bytes.toBytes("whatever"))); 182 region.put(new Put(Bytes.toBytes("obj3")).addColumn(fam, qual1, Bytes.toBytes("whatever")));
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/dports/www/webtrees/webtrees-1.7.18/webtrees/app/ |
H A D | Date.php | 42 public $qual1; variable in Fisharebest\\Webtrees\\Date 69 $this->qual1 = $match[1]; 74 $this->qual1 = $match[1]; 238 $q1 = $this->qual1; 239 $d1 = $this->date1->format($date_format, $this->qual1); 253 $d1tmp = $d1conv->format($date_format, $this->qual1); 427 $tmp->qual1 = $qualifier; 532 switch ($a->qual1) { 546 switch ($b->qual1) {
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/dports/devel/ppl/ppl-1.2/src/ |
H A D | checked_defs.hh | 127 #define PPL_DECLARE_FUN2_0_0(name, ret_type, qual1, type1, qual2, type2) \ argument 133 inline ret_type PPL_U(name)(PPL_U(qual1) PPL_U(type1)& arg1, \ 139 #define PPL_DECLARE_FUN2_0_1(name, ret_type, qual1, type1, \ argument 146 inline ret_type PPL_U(name)(PPL_U(qual1) PPL_U(type1)& arg1, \ 153 #define PPL_DECLARE_FUN2_0_2(name, ret_type, qual1, type1, qual2, type2, \ argument 160 inline ret_type PPL_U(name)(PPL_U(qual1) PPL_U(type1)& arg1, \ 167 #define PPL_DECLARE_FUN3_0_1(name, ret_type, qual1, type1, \ argument 174 inline ret_type PPL_U(name)(PPL_U(qual1) PPL_U(type1)& arg1, \ 184 qual1, type1, qual2, type2, qual3, type3, \ argument 284 #define PPL_SPECIALIZE_FUN2_0_0(name, func, ret_type, qual1, type1, \ argument [all …]
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/dports/biology/fastp/fastp-0.23.2/src/ |
H A D | basecorrector.cpp | 27 const char* qual1 = r1->mQuality->c_str(); in correctByOverlapAnalysis() local 42 if(qual1[p1] >= GOOD_QUAL && qual2[p2] <= BAD_QUAL) { in correctByOverlapAnalysis() 45 (*r2->mQuality)[p2] = qual1[p1]; in correctByOverlapAnalysis() 51 } else if(qual2[p2] >= GOOD_QUAL && qual1[p1] <= BAD_QUAL) { in correctByOverlapAnalysis()
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H A D | read.cpp | 223 const char* qual1 = mLeft->mQuality->c_str(); in fastMerge() local 243 if((qual1[offset+i]>='?' && qual2[i]<='0') || (qual1[offset+i]<='0' && qual2[i]>='?')){ in fastMerge() 270 if(qual1[offset+i]>='?' && qual2[i]<='0'){ in fastMerge() 272 mergedQual[offset+i] = qual1[offset+i]; in fastMerge() 279 mergedQual[offset+i] = qual1[offset+i] + qual2[i] - 33; in fastMerge()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seq_io/ |
H A D | test_stream_write_fasta.h | 118 CharString qual1 = "!!!!!"; in SEQAN_DEFINE_TEST() local 121 writeRecord(outStream, meta1, seq1, qual1, Fastq()); in SEQAN_DEFINE_TEST() 168 CharString qual1 = "!!!!!"; in SEQAN_DEFINE_TEST() local 171 writeRecord(outStream, meta1, seq1, qual1, Fastq(), SequenceOutputOptions(70, true)); in SEQAN_DEFINE_TEST()
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/dports/www/webtrees20/webtrees-2.0.19/webtrees/app/ |
H A D | Date.php | 52 public $qual1 = ''; variable in Fisharebest\\Webtrees\\Date 79 $this->qual1 = $match[1]; 84 $this->qual1 = $match[1]; 275 $q1 = $this->qual1; 276 $d1 = $this->date1->format($date_format, $this->qual1); 290 $d1tmp = $d1conv->format($date_format, $this->qual1); 467 $tmp->qual1 = $qualifier; 620 switch ($a->qual1) { 634 switch ($b->qual1) {
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/sra/ |
H A D | reader-illumina.c | 81 const SRAReaderColumn* qual1; member 98 options |= qual1 ? eQual1 : 0; in IlluminaReaderInit() 111 …(rc = SRAReader_FindColData(&self->dad, &IlluminaReader_master_columns_desc[5], &me->qual1, NULL))… in IlluminaReaderInit() 119 if( self->qual1 != NULL ) { in IlluminaReaderInit() 131 … bool read, bool qual1, bool qual4, bool intensity, bool noise, bool signal, bool qseq, in IlluminaReaderMake() argument 136 rc = IlluminaReaderInit(*self, read, qual1, qual4, intensity, noise, signal, qseq); in IlluminaReaderMake() 370 } else if( self->qual1 == NULL || self->qual1->size == 0 ) { in IlluminaReaderQuality1() 377 p = self->qual1->base; in IlluminaReaderQuality1() 384 p = self->qual1->base; in IlluminaReaderQuality1() 549 if( self->qual1 && self->qual1->size ) { [all …]
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/sra/ |
H A D | reader-illumina.c | 81 const SRAReaderColumn* qual1; member 98 options |= qual1 ? eQual1 : 0; in IlluminaReaderInit() 111 …(rc = SRAReader_FindColData(&self->dad, &IlluminaReader_master_columns_desc[5], &me->qual1, NULL))… in IlluminaReaderInit() 119 if( self->qual1 != NULL ) { in IlluminaReaderInit() 131 … bool read, bool qual1, bool qual4, bool intensity, bool noise, bool signal, bool qseq, in IlluminaReaderMake() argument 136 rc = IlluminaReaderInit(*self, read, qual1, qual4, intensity, noise, signal, qseq); in IlluminaReaderMake() 370 } else if( self->qual1 == NULL || self->qual1->size == 0 ) { in IlluminaReaderQuality1() 377 p = self->qual1->base; in IlluminaReaderQuality1() 384 p = self->qual1->base; in IlluminaReaderQuality1() 549 if( self->qual1 && self->qual1->size ) { [all …]
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/dports/biology/abyss/abyss-2.3.1/Align/ |
H A D | mergepairs.cc | 119 string qual1 = rec1.qual; in mergeReads() local 137 copy(qual1.begin(), qual1.begin() + overlap.overlap_t_pos, in mergeReads() 150 out_qual[pos] = max(qual1[pos], rc_qual2[i]); in mergeReads() 153 qual1[pos], rc_qual2[i]); in mergeReads() 154 out_qual[pos] = min(qual1[pos], rc_qual2[i]); in mergeReads()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/oligofar/ |
H A D | cquery.hpp | 50 …CQuery( CSeqCoding::ECoding coding, const string& id, const string& data1, const string& qual1, co… 105 …void x_InitColorspace( const string& id, const string& data1, const string& qual1, const string& d… 134 …ing::ECoding coding, const string& id, const string& data1, const string& qual1, const string& dat… in CQuery() argument 140 …case CSeqCoding::eCoding_ncbiqna: x_InitNcbiqna( id, data1 + qual1, data2 + qual2, base ); break; … in CQuery() 142 …case CSeqCoding::eCoding_colorsp: x_InitColorspace( id, data1, qual1, data2, qual2, base ); break;… in CQuery() 148 inline void CQuery::x_InitColorspace( const string& id, const string& data1, const string& qual1, c… in x_InitColorspace() argument 156 if( qual1.length() ) m_flags |= fStoresQuality0; in x_InitColorspace() 158 int q0 = qual1.length(); in x_InitColorspace() 176 for( unsigned i = 0, j = m_offset[0] + m_length[0]; i < qual1.length(); ) in x_InitColorspace() 177 m_data[j++] = qual1[i] + (33 - base); // SAM standard is 33 in x_InitColorspace()
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/dports/biology/bbmap/bbmap/current/shared/ |
H A D | TrimRead.java | 173 qual1=r.quality; in TrimRead() 175 assert(bases1!=null || qual1==null) : "\n"+new String(bases1)+"\n"+new String(qual1)+"\n"; in TrimRead() 176 …assert(bases1==null || qual1==null || bases1.length==qual1.length) : "\n"+new String(bases1)+"\n"+… in TrimRead() 229 qual2=qual1; in trim() 232 …qual2=((qual1==null || (trimLeft+trimRight>=qual1.length)) ? null : KillSwitch.copyOfRange(qual1, … in trim() 496 r.quality=qual1; in untrim() 818 public final byte[] qual1;
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