| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/fragments/ |
| H A D | FragmentUtilsUnitTest.java | 56 …final GATKRead read1 = makeOverlappingRead(leftFlank, HIGH_QUALITY, overlappingBases, overlappingB… in createAdjustFragmentsTest() local
65 …public void testAdjustingTwoReads(final GATKRead read1, final GATKRead read2, final int overlapSiz… in testAdjustingTwoReads()
100 …final GATKRead read1 = makeOverlappingRead(leftFlank, HIGH_QUALITY, overlappingBases, overlappingB… in createAdjustFragmentsTestSoftClips() local
111 …public void testAdjustingTwoReadsWithSoftClipping(final GATKRead read1, final GATKRead read2, fina… in testAdjustingTwoReadsWithSoftClipping()
147 …final GATKRead read1 = makeOverlappingRead(leftFlank, HIGH_QUALITY, overlappingBases, overlappingB… in createAdjustFragmentsTestSoftClipsInOverlapRegion() local
158 …public void testAdjustingTwoReadsWithSoftClippingOverlappingEachother(final GATKRead read1, final … in testAdjustingTwoReadsWithSoftClippingOverlappingEachother()
200 …final GATKRead read1 = makeOverlappingRead(leftFlank, HIGH_QUALITY, overlappingBases, overlappingB… in testLeadingIndelBehaviorForOverlappingReads() local
228 …final GATKRead read1 = makeOverlappingRead(leftFlank, HIGH_QUALITY, read1OverlappingRegion, read1O… in testIndelBehaviorForOverlappingReads() local
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | ReadQueryNameComparator.java | 17 public int compare(final GATKRead read1, final GATKRead read2) { in compare()
57 public int compareReadNames(final GATKRead read1, final GATKRead read2) { in compareReadNames()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/pileup/ |
| H A D | ReadPileupUnitTest.java | 50 final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header,"read1",0,1,10); in testSplitByReadGroup() local
152 final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1, 10); in testInvalidConstructorParametersReadsAndOffsetsLists() local
164 final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header,"read1",0,1,10); in testSplitByNullReadGroups() local
321 … final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, bases1, quals1, cigar1); in testSimplePileup() local
370 … final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, bases1, quals1, cigar1); in testSimplePileupWithIndelsOffset() local
428 … final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, bases1, quals1, cigar1); in testSimplePileupWithOffset() local
475 final GATKRead read1 = ArtificialReadUtils.createArtificialRead("6M"); in overlappingElementsToFix() local
611 final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "10M"); in testSortedIterator() local
623 Assert.assertSame(sortedIterator.next().getRead(), read1); in testSortedIterator() local
687 …final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1, readLength); in testGetPileup() local
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/qc/ |
| H A D | PileupUnitTest.java | 27 final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1, 10); in testInsertLengthOutput() local
51 final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1, 10); in testCreateVerboseOutput() local
|
| /dports/biology/py-cutadapt/cutadapt-3.3/src/cutadapt/ |
| H A D | filters.py | 40 def __call__(self, read1, read2, info1: ModificationInfo, info2: ModificationInfo) -> bool: argument
82 def update_statistics(self, read1, read2): argument
115 def __call__(self, read1, read2, info1: ModificationInfo, info2: ModificationInfo): argument
180 def _is_filtered_any(self, read1, read2, info1: ModificationInfo, info2: ModificationInfo): argument
183 def _is_filtered_both(self, read1, read2, info1: ModificationInfo, info2: ModificationInfo): argument
186 def _is_filtered_first(self, read1, read2, info1: ModificationInfo, info2: ModificationInfo): argument
189 def _is_filtered_second(self, read1, read2, info1: ModificationInfo, info2: ModificationInfo): argument
192 def __call__(self, read1, read2, info1: ModificationInfo, info2: ModificationInfo): argument
350 def __call__(self, read1, read2, info1: ModificationInfo, info2: ModificationInfo): argument
377 def __call__(self, read1, read2, info1, info2): argument
|
| /dports/devel/fbthrift/fbthrift-2021.12.27.00/thrift/lib/java/src/test/java/com/facebook/thrift/ |
| H A D | TCompactJSONTest.java | 59 StructWithAllTypes read1 = new StructWithAllTypes(); in testCompactJSONProtocol() local
119 StructWithMaps read1 = new StructWithMaps(); in testCompactJSONWithMaps() local
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/metrics/ |
| H A D | MeanQualityHistogramGeneratorUnitTest.java | 18 …GATKRead read1 = ArtificialReadUtils.createArtificialRead("aa".getBytes(), new byte[]{50, 50}, "2M… in testUsingQualities() local
83 …GATKRead read1 = ArtificialReadUtils.createArtificialRead("aa".getBytes(), new byte[]{50, 50}, "2M… in testUsingOriginalQualities() local
|
| /dports/biology/abyss/abyss-2.3.1/Unittest/Konnector/ |
| H A D | konnectorTest.cpp | 13 TEST(maskNew, read1) in TEST() argument
51 FastaRecord read1, read2; in TEST() local
|
| /dports/devel/p5-File-Slurp-Tiny/File-Slurp-Tiny-0.004/benchmark/ |
| H A D | 2.pl | 7 sub read1 { subroutine
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | QNameFinderTest.java | 36 final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 11074, in testHighDepthRegionFiltering() local
72 final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1, in testReadWithNegativeUnclippedStart() local
|
| /dports/games/libretro-fbneo/FBNeo-bbe3c05/src/burn/snd/ |
| H A D | burn_ym2203.h | 43 …#define BurnYM2203SetPorts(c, read0, read1, write0, write1) do { if (!DebugSnd_YM2203Initted) bpri… argument
46 …#define BurnYM2203SetPorts(c, read0, read1, write0, write1) AY8910SetPorts(c, read0, read1, write0… argument
|
| /dports/games/libretro-fbalpha/fbalpha-84eb9d9/src/burn/snd/ |
| H A D | burn_ym2203.h | 43 …#define BurnYM2203SetPorts(c, read0, read1, write0, write1) if (!DebugSnd_YM2203Initted) bprintf(P… argument
46 …#define BurnYM2203SetPorts(c, read0, read1, write0, write1) AY8910SetPorts(c, read0, read1, write0… argument
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/ |
| H A D | AlignmentContextUnitTest.java | 34 final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header,"read1",0,1,10); in test1Sample2Readgroups() local
102 final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header,"read1",0,1,10); in testNoSample() local
|
| /dports/databases/percona56-server/percona-server-5.6.51-91.0/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 59 char read1; variable
|
| /dports/databases/percona56-client/percona-server-5.6.51-91.0/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 59 char read1; variable
|
| /dports/databases/percona-pam-for-mysql/percona-server-5.6.51-91.0/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 59 char read1; variable
|
| /dports/databases/percona57-server/percona-server-5.7.36-39/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 59 char read1; variable
|
| /dports/databases/percona57-pam-for-mysql/percona-server-5.7.36-39/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 59 char read1; variable
|
| /dports/www/py-scrapy/Scrapy-2.5.1/scrapy/utils/ |
| H A D | gz.py | 13 def read1(gzf, size=-1): function
|
| /dports/databases/percona57-client/percona-server-5.7.36-39/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 59 char read1; variable
|
| /dports/databases/mysqlwsrep57-server/mysql-wsrep-wsrep_5.7.35-25.27/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 59 char read1; variable
|
| /dports/databases/xtrabackup/percona-xtrabackup-2.4.21/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 59 char read1; variable
|
| /dports/databases/mysqlwsrep56-server/mysql-wsrep-wsrep_5.6.51-25.33/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 59 char read1; variable
|
| /dports/databases/mysql56-client/mysql-5.6.51/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 59 char read1; variable
|
| /dports/databases/mysql55-client/mysql-5.5.62/storage/ndb/src/common/portlib/ |
| H A D | mmstest.cpp | 50 char read1; variable
|