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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/test/mpileup/
H A Dmpileup.tst33 # Command to execute. $pileup is replaced with the path to the pileup test
37 P mp_D.out $pileup mp_D.sam
38 P mp_D.out $pileup -m mp_D.sam
41 P mp_DI.out $pileup mp_DI.sam
47 P mp_I.out $pileup mp_I.sam
48 P mp_I.out $pileup -m mp_I.sam
49 P mp_P.out $pileup mp_P.sam
50 P mp_P.out $pileup -m mp_P.sam
53 P mp_ID.out $pileup mp_ID.sam
57 P mp_N.out $pileup mp_N.sam
[all …]
/dports/biology/htslib/htslib-1.14/test/mpileup/
H A Dmpileup.tst33 # Command to execute. $pileup is replaced with the path to the pileup test
37 P mp_D.out $pileup mp_D.sam
38 P mp_D.out $pileup -m mp_D.sam
41 P mp_DI.out $pileup mp_DI.sam
47 P mp_I.out $pileup mp_I.sam
48 P mp_I.out $pileup -m mp_I.sam
49 P mp_P.out $pileup mp_P.sam
50 P mp_P.out $pileup -m mp_P.sam
53 P mp_ID.out $pileup mp_ID.sam
57 P mp_N.out $pileup mp_N.sam
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/iterators/
H A DAllLocusIteratorUnitTest.java6 import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
62 locusIterator.forEachRemaining(pileup -> returnedPileups.add(pileup)); in testIteratorReturnsPileupsForAllLoci()
69 for ( final AlignmentContext pileup : returnedPileups ) { in testIteratorReturnsPileupsForAllLoci()
70 …Assert.assertEquals(pileup.getContig(), providedInterval.getContig(), "Wrong contig in returned pi… in testIteratorReturnsPileupsForAllLoci()
71 Assert.assertEquals(pileup.getStart(), position, "Wrong position in returned pileup"); in testIteratorReturnsPileupsForAllLoci()
73 if ( providedLoci.contains(pileup.getStart()) ) { in testIteratorReturnsPileupsForAllLoci()
74 …Assert.assertEquals(pileup.getBasePileup().size(), 10, "Didn't get back a pileup we provided expli… in testIteratorReturnsPileupsForAllLoci()
76 …Assert.assertEquals(pileup.getBasePileup().size(), 0, "Didn't get back an empty pileup where expec… in testIteratorReturnsPileupsForAllLoci()
79 … Assert.assertEquals(pileup.getEnd() - pileup.getStart() + 1, 1, "Returned pileup has wrong size"); in testIteratorReturnsPileupsForAllLoci()
82 …Assert.assertEquals(previousPileup.getContig(), pileup.getContig(), "Returned pileup has wrong con… in testIteratorReturnsPileupsForAllLoci()
[all …]
/dports/biology/sra-tools/sra-tools-2.11.0/test/pileup-stats/
H A DMakefile29 MODULE = test/pileup-stats
45 runtests: pileup-stats ignore-args
51 pileup-stats: $(BINDIR)/pileup-stats
53 …@ $(BINDIR)/pileup-stats -V | sed -e 's/\([1-9][0-9]*\)\.0\.0/\1/' -e 's/\([1-9][0-9]*\.[1-9][0-9]…
58 @ $(BINDIR)/pileup-stats --align-category primary ERR085308 >/dev/null
60 vg: $(BINDIR)/pileup-stats
62 valgrind --ncbi --suppressions=$(SRCDIR)/valgrind.suppress $(BINDIR)/pileup-stats -V
H A Dtest-ignore-args.sh29 if ! pileup-stats -L 1 2> /dev/null
34 if ! pileup-stats -z ignore.txt 2> /dev/null
39 if ! pileup-stats --log-level 1 2> /dev/null
44 if ! pileup-stats --xml-log ignore.txt 2> /dev/null
49 if ! pileup-stats --xml-log-fd ignore.txt 2> /dev/null
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/
H A DCSRA1_PileupEvent.c248 CSRA1_Pileup * pileup; in CSRA1_PileupEventGetAlignmentBase() local
274 if ( pileup -> ref_base == 0 ) in CSRA1_PileupEventGetAlignmentBase()
280 … ON_FAIL ( NGS_CursorCellDataDirect ( pileup -> ref . curs, ctx, pileup -> ref_chunk_id, in CSRA1_PileupEventGetAlignmentBase()
288 … pileup -> ref_chunk_xend - pileup -> ref . max_seq_len + row_len >= pileup -> slice_xend ); in CSRA1_PileupEventGetAlignmentBase()
292 …pileup -> ref_base = pileup -> ref_chunk_bases [ CSRA1_PileupEventGetPileup ( self ) -> ref_zpos %… in CSRA1_PileupEventGetAlignmentBase()
295 return pileup -> ref_base; in CSRA1_PileupEventGetAlignmentBase()
402 …int64_t ins_ref_last_id = ins_ref_last / pileup -> ref . max_seq_len + pileup -> reference_start_i… in CSRA1_PileupEventGetInsertionBases()
453 pileup -> ref_base = 0; in CSRA1_PileupEventGetInsertionBases()
617 … CSRA1_Pileup_AlignCursorData * cd = entry -> secondary ? & pileup -> sa : & pileup -> pa; in CSRA1_PileupEventGetIndelType()
872 assert ( pileup != NULL ); in CSRA1_PileupEventIteratorNext()
[all …]
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/
H A DCSRA1_PileupEvent.c248 CSRA1_Pileup * pileup; in CSRA1_PileupEventGetAlignmentBase() local
274 if ( pileup -> ref_base == 0 ) in CSRA1_PileupEventGetAlignmentBase()
280 … ON_FAIL ( NGS_CursorCellDataDirect ( pileup -> ref . curs, ctx, pileup -> ref_chunk_id, in CSRA1_PileupEventGetAlignmentBase()
288 … pileup -> ref_chunk_xend - pileup -> ref . max_seq_len + row_len >= pileup -> slice_xend ); in CSRA1_PileupEventGetAlignmentBase()
292 …pileup -> ref_base = pileup -> ref_chunk_bases [ CSRA1_PileupEventGetPileup ( self ) -> ref_zpos %… in CSRA1_PileupEventGetAlignmentBase()
295 return pileup -> ref_base; in CSRA1_PileupEventGetAlignmentBase()
402 …int64_t ins_ref_last_id = ins_ref_last / pileup -> ref . max_seq_len + pileup -> reference_start_i… in CSRA1_PileupEventGetInsertionBases()
453 pileup -> ref_base = 0; in CSRA1_PileupEventGetInsertionBases()
617 … CSRA1_Pileup_AlignCursorData * cd = entry -> secondary ? & pileup -> sa : & pileup -> pa; in CSRA1_PileupEventGetIndelType()
872 assert ( pileup != NULL ); in CSRA1_PileupEventIteratorNext()
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/qc/
H A DPileupUnitTest.java5 import org.broadinstitute.hellbender.utils.pileup.PileupElement;
6 import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
32 final ReadPileup pileup = new ReadPileup(loc, Arrays.asList(read1, read2), 1); in testInsertLengthOutput() local
34 Assert.assertEquals(Pileup.insertLengthOutput(pileup.makeFilteredPileup( in testInsertLengthOutput()
36 Assert.assertEquals(Pileup.insertLengthOutput(pileup.makeFilteredPileup( in testInsertLengthOutput()
39 Assert.assertEquals(Pileup.insertLengthOutput(pileup), "100,50"); in testInsertLengthOutput()
63 final ReadPileup pileup = new ReadPileup(loc, Arrays.asList(pe1, pe2)); in testCreateVerboseOutput() local
66 Assert.assertEquals(Pileup.createVerboseOutput(pileup.makeFilteredPileup( in testCreateVerboseOutput()
68 Assert.assertEquals(Pileup.createVerboseOutput(pileup.makeFilteredPileup( in testCreateVerboseOutput()
71 Assert.assertEquals(Pileup.createVerboseOutput(pileup), "1 "+read1String+","+read2String); in testCreateVerboseOutput()
/dports/biology/vt/vt-0.57721/
H A Ddiscover.cpp107 Pileup pileup; member in __anon78be79810111::Igor
943 if (bam_get_pos1(s)-pileup.get_window_size()>pileup.get_gbeg1()) in flushable()
967 uint32_t lend0 = pileup.get_gend1()<gpos1 ? pileup.end() : pileup.g2i(gpos1); in flush()
980 for (i=pileup.begin(); i!=lend0; i=pileup.inc(i,1)) in flush()
1007 for (i=pileup.begin(); i!=pileup.end(); i=pileup.inc(i,1)) in flush()
1033 for (i=pileup.begin(); i!=pileup.end(); i=pileup.inc(i,1)) in flush()
1042 pileup.set_tid(-1); in flush()
1043 pileup.set_gbeg1(0); in flush()
1044 pileup.set_beg0(0); in flush()
1045 pileup.set_end0(0); in flush()
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/
H A DByteMapIntervalPileup.java288 private final ByteMapIntervalPileup pileup; field in ByteMapIntervalPileup.Element
291 this.pileup = pileup; in Element()
301 Arrays.fill(pileup.bases[row], maxColumn + 1, pileup.width, NO_BASE); in Element()
302 Arrays.fill(pileup.quals[row], 0, minColumn, NO_BQ); in Element()
303 Arrays.fill(pileup.quals[row], maxColumn + 1, pileup.width, NO_BQ); in Element()
305 pileup.insertsBuffer.clear(); in Element()
306 pileup.insertsBufferOffsets.clear(); in Element()
343 mergeAdjacentInserts(read, pileup.insertsBuffer, pileup.insertsBufferOffsets); in Element()
344 inserts = consolidateInserts(pileup.insertsBuffer, pileup.insertsBufferOffsets); in Element()
459 return pileup.bases[row][column];
[all …]
/dports/biology/sra-tools/sra-tools-2.11.0/test/ngs-pileup/
H A DMakefile29 MODULE = test/ngs-pileup
32 test-ngs-pileup
47 test-ngs-pileup
59 $(TEST_BINDIR)/test-ngs-pileup: $(TEST_NGS_PILEUP_OBJ)
66 slowtests: diff-vs-sra-pileup
68 diff-vs-sra-pileup:
137 .PHONY: diff-vs-sra-pileup
/dports/biology/py-macs2/MACS-2.2.7.1/MACS2/
H A DcPosValCalculation.c78 int p, pre_p, pileup; in single_end_pileup() local
120 int p, pre_p, pileup; in quick_pileup() local
131 pileup = 0; in quick_pileup()
158 pileup += 1; in quick_pileup()
172 pileup -= 1; in quick_pileup()
198 pileup -= 1; in quick_pileup()
439 int p, pre_p, pileup; in quick_pileup_simple() local
450 pileup = 0; in quick_pileup_simple()
474 pileup += 1; in quick_pileup_simple()
488 pileup -= 1; in quick_pileup_simple()
[all …]
H A DPileup.pyx173 # Unified pileup function #
644 pileup = 0
656 pre_v = pileup
671 pileup += 1
683 pileup -= 1
703 pileup -= 1
773 pileup = 0
785 pre_v = pileup
797 pileup += 1
811 pileup -= 1
[all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/
H A DAlignmentContextUnitTest.java8 import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
49 …final ReadPileup pileup = new ReadPileup(loc, Arrays.asList(read1, read2, read3, read4, read5, rea… in test1Sample2Readgroups() local
51 final AlignmentContext ac = new AlignmentContext(loc, pileup); in test1Sample2Readgroups()
52 Assert.assertSame(ac.getBasePileup(), pileup); in test1Sample2Readgroups() local
59 Assert.assertEquals(ac.size(), pileup.size()); in test1Sample2Readgroups()
65 … Assert.assertEquals((Iterable<?>) acFWD.getBasePileup(), (Iterable<?>)pileup, "Forward Pileup"); in test1Sample2Readgroups()
87 …mentContext> stringAlignmentContextMap = AlignmentContext.splitContextBySampleName(pileup, header); in test1Sample2Readgroups()
90 Assert.assertEquals(stringAlignmentContextMap.get("sample1").getBasePileup(), pileup); in test1Sample2Readgroups()
105 final ReadPileup pileup = new ReadPileup(loc, Arrays.asList(read1), 1); in testNoSample() local
106 final AlignmentContext ac = new AlignmentContext(loc, pileup); in testNoSample()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/qc/
H A DCheckPileup.java14 import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
130 final ReadPileup pileup = context.getBasePileup(); in apply() local
134 pileup.fixOverlaps(); in apply()
138 …out.printf("No truth pileup data available at %s%n", pileup.getPileupString((char) ref.getBase())); in apply()
142 context.getLocation(), new String(pileup.getBases()))); in apply()
145 final String pileupDiff = pileupDiff(pileup, truePileup); in apply()
147 …out.printf("%s vs. %s%n", pileup.getPileupString((char) ref.getBase()), truePileup.getPileupString… in apply()
154 nBases += pileup.size(); in apply()
H A DPileup.java14 import org.broadinstitute.hellbender.utils.pileup.PileupElement;
15 import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
187 static String insertLengthOutput(final ReadPileup pileup) { in insertLengthOutput() argument
188 return pileup.getReads().stream() in insertLengthOutput()
199 static String createVerboseOutput(final ReadPileup pileup) { in createVerboseOutput() argument
202 sb.append(pileup.getNumberOfElements(PileupElement::isDeletion)); in createVerboseOutput()
204 for (final PileupElement p : pileup) { in createVerboseOutput()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/
H A DSomaticReferenceConfidenceModel.java14 import org.broadinstitute.hellbender.utils.pileup.PileupElement;
15 import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
59 final ReadPileup pileup, in calcGenotypeLikelihoodsOfRefVsAny() argument
67 perSampleReadMap.put(samples.getSample(0), pileup.getReads()); in calcGenotypeLikelihoodsOfRefVsAny()
69 final List<Byte> altQuals = new ArrayList<>(pileup.size() / 20); in calcGenotypeLikelihoodsOfRefVsAny()
71 for (final PileupElement element : pileup) { in calcGenotypeLikelihoodsOfRefVsAny()
98 …public void doIndelRefConfCalc(final int ploidy, final byte[] ref, final ReadPileup pileup, final … in doIndelRefConfCalc() argument
/dports/biology/py-macs2/MACS-2.2.7.1/test/
H A Dtest_Pileup.py60 … self.pileup = unified_pileup_bdg(self.fwtrack2, self.d, self.scale_factor, halfextension=False)
62 chrs = self.pileup.get_chr_names()
64 (p,v) = self.pileup.get_data_by_chr(chrom)
85 …self.pileup = unified_pileup_bdg(self.fwtrack2, self.d_s, self.scale_factor_s, baseline_value=13, …
87 chrs = self.pileup.get_chr_names()
89 (p,v) = self.pileup.get_data_by_chr(chrom)
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/examples/
H A DMakefile2 ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz ex1.bcf calDepth
11 ex1.pileup.gz:ex1.bam ex1.fa
12 ../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
14 ../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
46 rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf
/dports/biology/sra-tools/sra-tools-2.11.0/tools/ngs-pileup/
H A DMakefile30 MODULE = tools/ngs-pileup
33 ngs-pileup \
65 ngs-pileup \
81 $(BINDIR)/ngs-pileup: $(NGS_PILEUP_OBJ)
/dports/biology/sra-tools/sra-tools-2.11.0/test/driver-tool/expected/
H A Dsra-pileup.stderr1 sra-pileup SRR000001
2 sra-pileup ERR000001
3 sra-pileup DRR000001
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/
H A DPileupSpark.java22 import org.broadinstitute.hellbender.utils.pileup.PileupElement;
23 import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
196 private static String insertLengthOutput(final ReadPileup pileup) { in insertLengthOutput() argument
197 return pileup.getReads().stream() in insertLengthOutput()
202 private static String createVerboseOutput(final ReadPileup pileup) { in createVerboseOutput() argument
205 sb.append(pileup.getNumberOfElements(PileupElement::isDeletion)); in createVerboseOutput()
207 for (final PileupElement p : pileup) { in createVerboseOutput()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/
H A DASEReadCounter.java19 import org.broadinstitute.hellbender.utils.pileup.PileupElement;
20 import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
211 final ReadPileup pileup = filterPileup(alignmentContext.getBasePileup(), countType); in apply() local
214 final String line = calculateLineForSite(pileup, siteID, refAllele, altAllele); in apply()
244 …private String calculateLineForSite(final ReadPileup pileup, final String siteID, final char refAl… in calculateLineForSite() argument
248 for (final PileupElement base : pileup) { in calculateLineForSite()
283 line.append(pileup.getLocation().getContig()).append(separator); in calculateLineForSite()
284 line.append(pileup.getLocation().getStart()).append(separator); in calculateLineForSite()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/readorientation/
H A DF1R2CountsCollector.java17 import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
85 public void process(final ReadPileup pileup, final ReferenceContext referenceContext) { in process() argument
106 …pileup.makeFilteredPileup(pe -> Objects.equals(ReadUtils.getSampleName(pe.getRead(), header), only… in process()
107 : pileup.splitBySample(header, null); in process()
197 private boolean isPileupGood(final ReadPileup pileup){ in isPileupGood() argument
198 final int[] baseCounts = pileup.getBaseCounts(); in isPileupGood()
201 List<Integer> mappingQualities = Ints.asList(pileup.getMappingQuals()); in isPileupGood()
205 …boolean isIndel = pileup.getNumberOfElements(pe -> pe.isDeletion() || pe.isAfterInsertion() || pe.… in isPileupGood()
209 isIndel = isIndel || depth == 0 && pileup.size() > 0; in isPileupGood()
/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-pileup/
H A DMakefile29 MODULE = tools/sra-pileup
34 sra-pileup \
83 sra-pileup
94 $(BINDIR)/sra-pileup: $(TOOL_OBJ)

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