SafinaAr
commented
5 years ago I also tried to build gradlew present in the ximmer folder getting these errors:
:compileGroovy
startup failed:
/home/sark/ximmer/src/main/groovy/AngelResults.groovy: 4: unable to resolve class gngs.RangedData
@ line 4, column 1.
import gngs.RangedData
^
/home/sark/ximmer/src/main/groovy/CNMopsResults.groovy: 5: unable to resolve class gngs.RangedData
@ line 5, column 1.
import gngs.RangedData
^
/home/sark/ximmer/src/main/groovy/CNMopsResults.groovy: 6: unable to resolve class gngs.Region
@ line 6, column 1.
import gngs.Region
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 8: unable to resolve class org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction
@ line 8, column 1.
import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 7: unable to resolve class org.apache.commons.math3.analysis.interpolation.LoessInterpolator
@ line 7, column 1.
import org.apache.commons.math3.analysis.interpolation.LoessInterpolator
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 20: unable to resolve class htsjdk.samtools.SamReader
@ line 20, column 1.
import htsjdk.samtools.SamReader
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 13: unable to resolve class graxxia.Matrix
@ line 13, column 1.
import graxxia.Matrix
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 14: unable to resolve class graxxia.Stats
@ line 14, column 1.
import graxxia.Stats
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 39: unable to resolve class SampleInfo
@ line 39, column 16.
Map<String,SampleInfo> sampleInfo
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 41: unable to resolve class Regions
@ line 41, column 5.
Regions cnvs
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 56: unable to resolve class SAM
@ line 56, column 16.
Map<String,SAM> bams
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 61: unable to resolve class RangedData
@ line 61, column 17.
Map<String, RangedData> cnvCalls
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 69: unable to resolve class RefGenes
@ line 69, column 5.
RefGenes geneDb = null
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 71: unable to resolve class Regions
@ line 71, column 5.
Regions targetRegions = null
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 73: unable to resolve class Regions
@ line 73, column 16.
Map<String,Regions> vcfs = Collections.synchronizedMap([:])
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 78: unable to resolve class Regions
@ line 78, column 5.
Regions amplicons = null
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 762: unable to resolve class htsjdk.samtools.SamReader
@ line 762, column 29.
ThreadLocal<Map<String, SamReader>> readers = new ThreadLocal()
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 112: unable to resolve class Regions
@ line 112, column 16.
CNVDiagram(Regions cnvs, Map<String,SampleInfo> sampleInfo, Map<String, RangedData> cnvCalls, Regions targetRegions, List<String> vcfFiles, List<String> samples=null) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 112: unable to resolve class SampleInfo
@ line 112, column 41.
gram(Regions cnvs, Map<String,SampleInfo
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 112: unable to resolve class RangedData
@ line 112, column 77.
Info> sampleInfo, Map<String, RangedData
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 112: unable to resolve class Regions
@ line 112, column 99.
String, RangedData> cnvCalls, Regions ta
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 131: unable to resolve class VCF
@ line 131, column 14.
List<VCF> vcfs = vcfFiles.collect { VCF.parse(it) { cnvs.overlaps(it) } }
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 133: unable to resolve class VCF
@ line 133, column 13.
Map<VCF, Regions> vcfRegions = vcfs.collectEntries { [ it, it.toRegions() ] }
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 133: unable to resolve class Regions
@ line 133, column 18.
Map<VCF, Regions> vcfRegions = vcfs.collectEntries { [ it, it.toRegions() ] }
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 136: unable to resolve class VCF
@ line 136, column 17.
VCF sampleVCF = vcfs.find { sample in it.samples }
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 142: unable to resolve class SAM
@ line 142, column 14.
List<SAM> sampleBams = allSamples.collect { String sample ->
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 147: unable to resolve class SAM
@ line 147, column 13.
new SAM(sampleInfo[sample].files.bam[0])
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 161: unable to resolve class Regions
@ line 161, column 21.
Regions meanRegions = targetRegions
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 243: unable to resolve class Region
@ line 243, column 18.
void drawCNV(Region cnv, String outputFileBase, int width, int height, List callers, Map colors) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 284: unable to resolve class SAM
@ line 284, column 13.
SAM bam = bams[cnv.sample]
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 298: unable to resolve class Region
@ line 298, column 16.
Region displayRegion = new Region(cnv.chr, froms[0]..tos[-1])
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 298: unable to resolve class Region
@ line 298, column 32.
Region displayRegion = new Region(cnv.chr, froms[0]..tos[-1])
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 303: unable to resolve class graxxia.Drawing
@ line 303, column 25.
graxxia.Drawing d
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 312: unable to resolve class Region
@ line 312, column 20.
Region targetRegion = new Region(cnv.chr, target)
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 312: unable to resolve class Region
@ line 312, column 35.
Region targetRegion = new Region(cnv.chr, target)
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 444: unable to resolve class graxxia.Drawing
@ line 444, column 35.
void drawInterpolatedCoverage(graxxia.Drawing d, Matrix coverage, IntRange target, double [] targetRange) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 465: unable to resolve class graxxia.Drawing
@ line 465, column 36.
void drawVariants(Writer json, graxxia.Drawing d, Region cnv, List<IntRange> targets) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 465: unable to resolve class Region
@ line 465, column 55.
iter json, graxxia.Drawing d, Region cnv
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 467: unable to resolve class Regions
@ line 467, column 17.
Regions vcf = vcfs[cnv.sample]
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 476: unable to resolve class Variant
@ line 476, column 9.
for(Variant variant in variants) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 514: unable to resolve class Region
@ line 514, column 48.
rgetJSONCoverage(Writer json, Region tar
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 525: unable to resolve class Region
@ line 525, column 62.
amFrame(String imageFileName, Region dis
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 525: unable to resolve class graxxia.Drawing
@ line 525, column 5.
graxxia.Drawing createDiagramFrame(String imageFileName, Region displayRegion, List<IntRange> targets, int width, int height) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 530: unable to resolve class graxxia.Drawing
@ line 530, column 25.
graxxia.Drawing d = new graxxia.Drawing(
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 530: unable to resolve class graxxia.Drawing
@ line 530, column 29.
graxxia.Drawing d = new graxxia.Drawing(
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 567: unable to resolve class Region
@ line 567, column 40.
List<IntRange> determineCnvTargets(Region rawCNV, List<String> genes) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 578: unable to resolve class Region
@ line 578, column 16.
Region cnv = new Region(rawCNV.chr, cnvTargetIntersect[0].from, cnvTargetIntersect[-1].to)
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 578: unable to resolve class Region
@ line 578, column 22.
Region cnv = new Region(rawCNV.chr, cnvTargetIntersect[0].from, cnvTargetIntersect[-1].to)
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 619: unable to resolve class Region
@ line 619, column 28.
List<Range> padTargets(Region cnv, List<Range> targets) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 659: unable to resolve class Region
@ line 659, column 67.
xonsRange(List<String> genes, Region cnv
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 661: unable to resolve class Regions
@ line 661, column 17.
Regions geneExons = genes.sum { geneDb.getExons(it) }.reduce().grep { it.chr == cnv.chr } as Regions
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 661: unable to resolve class Regions
@ line 661, column 99.
().grep { it.chr == cnv.chr } as Regions
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 689: unable to resolve class graxxia.Drawing
@ line 689, column 24.
void drawAmplicons(graxxia.Drawing d, Region cnv) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 689: unable to resolve class Region
@ line 689, column 43.
wAmplicons(graxxia.Drawing d, Region cnv
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 702: unable to resolve class Region
@ line 702, column 14.
List<Region> cnvAmplicons = this.amplicons[indices]
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 728: unable to resolve class Region
@ line 728, column 34.
Matrix getNormalisedCoverage(Region region, String sample) {
^
:compileGroovy FAILED
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 748: unable to resolve class Region
@ line 748, column 34.
def Matrix normaliseCoverage(Region region) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 765: unable to resolve class Region
@ line 765, column 30.
Matrix getCoverageMatrix(Region region) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 779: unable to resolve class PileupIterator
@ line 779, column 28.
PileupIterator pileup
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 782: unable to resolve class PileupIterator.Pileup
@ line 782, column 48.
ef sampleCov = pileup.collect { PileupIt
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 816: unable to resolve class RangedData
FAILURE: Build failed with an exception.
@ line 816, column 93.
, Closure factory, Map<String,RangedData
* What went wrong:
^
Execution failed for task ':compileGroovy'.
> Compilation failed; see the compiler error output for details.
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 835: unable to resolve class Cli
@ line 835, column 13.
* Try:
Cli cli = new Cli(usage: "CNVDiagram <options>")
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 835: unable to resolve class Cli
@ line 835, column 19.
BUILD FAILED
Cli cli = new Cli(usage: "CNVDiagram <options>")
^
Total time: 10.455 secs
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 875: unable to resolve class RangedData
@ line 875, column 20.
Map<String,RangedData> cnvCalls = [:]
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 902: unable to resolve class BED
@ line 902, column 27.
def bed = new BED(bedFile, withExtra:true).load()
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 903: unable to resolve class Regions
@ line 903, column 34.
cnvCalls[name] = new Regions()
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 936: unable to resolve class Regions
@ line 936, column 17.
Regions targetRegions = new BED(opts.targets).load().reduce()
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 936: unable to resolve class BED
@ line 936, column 33.
Regions targetRegions = new BED(opts.targets).load().reduce()
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 976: unable to resolve class RefGenes
@ line 976, column 30.
diagram.geneDb = new RefGenes(opts.refseq, stripChr: cnvs.numberOfRanges>0 && !cnvs[0].chr.startsWith('chr'))
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 980: unable to resolve class BED
@ line 980, column 33.
diagram.amplicons = new BED(opts.amplicons,withExtra:true).load()
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1003: unable to resolve class Regions
@ line 1003, column 5.
private static Regions loadCNVs(OptionAccessor opts) {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1004: unable to resolve class Regions
@ line 1004, column 17.
Regions cnvs
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1010: unable to resolve class Region
@ line 1010, column 20.
Region cnv = new Region(parts[2])
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1010: unable to resolve class Region
@ line 1010, column 27.
Region cnv = new Region(parts[2])
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1014: unable to resolve class Regions
@ line 1014, column 20.
cnvs = new Regions()
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1019: unable to resolve class Regions
@ line 1019, column 20.
cnvs = new Regions()
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1020: unable to resolve class Region
@ line 1020, column 60.
, withExtra:true).load().each { Region r
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1020: unable to resolve class BED
@ line 1020, column 13.
new BED(opts.cnvs, withExtra:true).load().each { Region r ->
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1027: unable to resolve class RangedData
@ line 1027, column 20.
cnvs = new RangedData(opts.cnvs).load()
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1030: unable to resolve class Regions
@ line 1030, column 53.
s.grep { it.chr == opts.chr } as Regions
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1036: unable to resolve class Regions
@ line 1036, column 5.
private Regions findLiteMeanRegions() {
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1040: unable to resolve class Regions
@ line 1040, column 16.
Regions result = new Regions()
^
/home/sark/ximmer/src/main/groovy/CNVDiagram.groovy: 1040: unable to resolve class Regions
@ line 1040, column 25.
Regions result = new Regions()
^
/home/sark/ximmer/src/main/groovy/CNVResults.groovy: 1: unable to resolve class gngs.RangedData
@ line 1, column 1.
import gngs.RangedData
^
/home/sark/ximmer/src/main/groovy/CNVResults.groovy: 27: unable to resolve class TargetedCNVAnnotator
@ line 27, column 19.
String toJson(TargetedCNVAnnotator annotator = null) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 10: unable to resolve class htsjdk.samtools.SAMTagUtil
@ line 10, column 1.
import htsjdk.samtools.SAMTagUtil;
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 8: unable to resolve class htsjdk.samtools.SAMFileWriter
@ line 8, column 1.
import htsjdk.samtools.SAMFileWriter;
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 9: unable to resolve class htsjdk.samtools.SAMRecord
@ line 9, column 1.
import htsjdk.samtools.SAMRecord;
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 38: unable to resolve class SAM
@ line 38, column 5.
SAM maleBam
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 40: unable to resolve class SAM
@ line 40, column 5.
SAM femaleBam
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 76: unable to resolve class DGV
@ line 76, column 5.
DGV dgv = null
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 90: unable to resolve class Regions
@ line 90, column 5.
private Regions targetRegions = null
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 99: unable to resolve class Regions
@ line 99, column 25.
public CNVSimulator(Regions targetRegions, String femaleBam, String maleBam) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 100: unable to resolve class SAM
@ line 100, column 29.
this(targetRegions, new SAM(femaleBam), maleBam != null ? new SAM(maleBam) : null)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 100: unable to resolve class SAM
@ line 100, column 67.
femaleBam), maleBam != null ? new SAM(ma
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 103: unable to resolve class Regions
@ line 103, column 25.
public CNVSimulator(Regions targetRegions, SAM femaleBam, SAM maleBam) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 103: unable to resolve class SAM
@ line 103, column 48.
ulator(Regions targetRegions, SAM female
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 103: unable to resolve class SAM
@ line 103, column 63.
targetRegions, SAM femaleBam, SAM maleBa
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 125: unable to resolve class Cli
@ line 125, column 13.
Cli cli = new Cli(usage:"CNVSimulator [options]")
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 125: unable to resolve class Cli
@ line 125, column 19.
Cli cli = new Cli(usage:"CNVSimulator [options]")
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 155: unable to resolve class BED
@ line 155, column 41.
simulator.setTargetCoverage(new BED(op
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 168: unable to resolve class Region
@ line 168, column 61.
ts.o, new Regions().addRegion(new Region
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 168: unable to resolve class Regions
@ line 168, column 37.
simulator.createBam(opts.o, new Regions().addRegion(new Region(opts.region)))
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 172: unable to resolve class SAM
@ line 172, column 28.
int countAutosomeReads(SAM bam) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 197: unable to resolve class Regions
@ line 197, column 25.
Regions autosomalRegions = null
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 206: unable to resolve class ProgressCounter
@ line 206, column 33.
ProgressCounter counter = new ProgressCounter()
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 206: unable to resolve class ProgressCounter
@ line 206, column 43.
ProgressCounter counter = new Progre
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 243: unable to resolve class Regions
@ line 243, column 43.
ateBam(String outputFileName, Regions re
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 270: unable to resolve class Regions
@ line 270, column 39.
List<SAMRecordPair> loadMaleReads(Regions cleanRegions) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 270: unable to resolve class SAMRecordPair
@ line 270, column 10.
List<SAMRecordPair> loadMaleReads(Regions cleanRegions) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 273: unable to resolve class SAMRecordPair
@ line 273, column 14.
List<SAMRecordPair> maleRegionReads = []
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 274: unable to resolve class Region
@ line 274, column 9.
for(Region cleanRegion in cleanRegions) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 276: unable to resolve class SAMRecordPair
@ line 276, column 31.
SAMRecordPair pair = new SAMRecordPair(r1:r1,r2:r2)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 276: unable to resolve class SAMRecordPair
@ line 276, column 38.
SAMRecordPair pair = new SAMRecordPair(r1:r1,r2:r2)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 286: unable to resolve class SAMRecordPair
@ line 286, column 37.
return maleRegionReads.sort { SAMRecordPair pair -> pair.r1.alignmentStart }
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 299: unable to resolve class Regions
@ line 299, column 56.
cement(String outputFileName, Regions cl
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 303: unable to resolve class SAMRecordPair
@ line 303, column 14.
List<SAMRecordPair> maleRegionReads = loadMaleReads(cleanRegions)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 313: unable to resolve class ProgressCounter
@ line 313, column 25.
ProgressCounter writeProgress = new ProgressCounter()
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 313: unable to resolve class ProgressCounter
@ line 313, column 41.
ogressCounter writeProgress = new Progre
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 318: unable to resolve class SAMRecordPair
@ line 318, column 18.
Iterator<SAMRecordPair> nextMaleRegionReadIterator = maleRegionReads.iterator()
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 319: unable to resolve class SAMRecordPair
@ line 319, column 23.
SAMRecordPair nextMaleReadPair = nextMaleRegionReadIterator.next()
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 321: unable to resolve class SAMRecordPair
@ line 321, column 31.
Closure setPairInfo = { SAMRecordPair pair ->
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 330: unable to resolve class SAMRecordPair
@ line 330, column 34.
SAMRecordPair pair = nextMaleRegionReadIterator.next()
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 341: unable to resolve class SAMRecordPair
@ line 341, column 96.
: flushReads, spoolSize:8000) { SAMRecor
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 343: unable to resolve class SAMRecordPair
@ line 343, column 18.
List<SAMRecordPair> result = []
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 364: unable to resolve class SAMRecordPair
@ line 364, column 41.
ordPair extractMaleReadsUntil(SAMRecordP
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 364: unable to resolve class SAMRecordPair
@ line 364, column 71.
SAMRecordPair start, Iterator<SAMRecordP
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 364: unable to resolve class SAMRecordPair
@ line 364, column 92.
Iterator<SAMRecordPair> iter, SAMRecordP
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 364: unable to resolve class SAMRecordPair
@ line 364, column 117.
ter, SAMRecordPair pair, List<SAMRecordP
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 363: unable to resolve class SAMRecordPair
@ line 363, column 5.
@CompileStatic
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 366: unable to resolve class SAMRecordPair
@ line 366, column 22.
SAMRecordPair nextMaleReadPair = start
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 383: unable to resolve class Regions
@ line 383, column 59.
entOld(String outputFileName, Regions cl
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 387: unable to resolve class SAMRecordPair
@ line 387, column 14.
List<SAMRecordPair> maleRegionReads = loadMaleReads(cleanRegions)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 398: unable to resolve class ProgressCounter
@ line 398, column 25.
ProgressCounter writeProgress = new ProgressCounter()
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 398: unable to resolve class ProgressCouter
@ line 398, column 41.
ogressCounter writeProgress = new Progre
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 451: unable to resolve class SAMRecordPair
@ line 451, column 26.
boolean isPairBefore(SAMRecordPair pair1, SAMRecordPair pair2) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 451: unable to resolve class SAMRecordPair
@ line 451, column 47.
irBefore(SAMRecordPair pair1, SAMRecordP
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 463: unable to resolve class Regions
@ line 463, column 55.
Sample(String outputFileName, Regions cl
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 478: unable to resolve class SAMRecordPair
@ line 478, column 63.
airs(options, outputFileName) { SAMRecor
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 532: unable to resolve class Regions
@ line 532, column 28.
Region findCleanRegion(Regions fromRegions, Region seedRegion) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 532: unable to resolve class Region
@ line 532, column 49.
anRegion(Regions fromRegions, Region see
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 532: unable to resolve class Region
@ line 532, column 5.
Region findCleanRegion(Regions fromRegions, Region seedRegion) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 535: unable to resolve class Regions
@ line 535, column 17.
Regions seedWindow = fromRegions.window(seedRegion, 10).grep { it.chr == seedRegion.chr } as Regions
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 535: unable to resolve class Regions
@ line 535, column 99.
{ it.chr == seedRegion.chr } as Regions
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 545: unable to resolve class Regions
@ line 545, column 17.
Regions maleReadRegions
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 547: unable to resolve class SAM
@ line 547, column 17.
SAM maleRegionBam = new SAM(maleBam.samFile)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 547: unable to resolve class SAM
@ line 547, column 33.
SAM maleRegionBam = new SAM(maleBam.samFile)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 557: unable to resolve class Regions
@ line 557, column 17.
Regions femaleReadRegions = femaleBam.toPairRegions(chromosome,seedWindow[0].from,seedWindow[-1].to,500)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 562: unable to resolve class Regions
@ line 562, column 17.
Regions combinedRegions = maleReadRegions ? maleReadRegions.reduce() : new Regions()
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 562: unable to resolve class Regions
@ line 562, column 80.
? maleReadRegions.reduce() : new Region
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 572: unable to resolve class Regions
@ line 572, column 21.
Regions testRegions = femaleBam.toPairRegions(chromosome,seedWindow[0].from,seedWindow[-1].to,500)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 578: unable to resolve class Region
@ line 578, column 16.
Region result = new Region(chromosome, overlaps*.from.min()..overlaps*.to.max())
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 578: unable to resolve class Region
@ line 578, column 25.
Region result = new Region(chromosome, overlaps*.from.min()..overlaps*.to.max())
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 595: unable to resolve class Regions
@ line 595, column 25.
Region selectRegion(Regions fromRegions, int numRanges, Exclusions excludeRegions=null) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 595: unable to resolve class Region
@ line 595, column 5.
Region selectRegion(Regions fromRegions, int numRanges, Exclusions excludeRegions=null) {
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 597: unable to resolve class Region
@ line 597, column 16.
Region cleanRegion = null
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 626: unable to resolve class Region
@ line 626, column 20.
Region seedRegion = new Region(chromosome,r)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 626: unable to resolve class Region
@ line 626, column 33.
Region seedRegion = new Region(chromosome,r)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 633: unable to resolve class Region
@ line 633, column 24.
Region candidateCleanRegion = findCleanRegion(fromRegions, seedRegion)
^
/home/sark/ximmer/src/main/groovy/CNVSimulator.groovy: 665: unable to resolve class Region
@ line 665, column 40.
boolean isOverlappingPopulationCNV(Region regionToCheck) {
^
/home/sark/ximmer/src/main/groovy/CodexResults.groovy: 5: unable to resolve class gngs.RangedData
@ line 5, column 1.
import gngs.RangedData
^
/home/sark/ximmer/src/main/groovy/CodexResults.groovy: 6: unable to resolve class gngs.Region
@ line 6, column 1.
import gngs.Region
^
/home/sark/ximmer/src/main/groovy/ConiferResults.groovy: 5: unable to resolve class gngs.RangedData
@ line 5, column 1.
import gngs.RangedData
^
/home/sark/ximmer/src/main/groovy/ConiferResults.groovy: 6: unable to resolve class gngs.Region
@ line 6, column 1.
import gngs.Region
^
/home/sark/ximmer/src/main/groovy/ExcavatorResults.groovy: 5: unable to resolve class gngs.RangedData
@ line 5, column 1.
import gngs.RangedData
^
/home/sark/ximmer/src/main/groovy/ExcavatorResults.groovy: 6: unable to resolve class gngs.Region
@ line 6, column 1.
import gngs.Region
^
/home/sark/ximmer/src/main/groovy/GATKMeanEstimator.groovy: 35: unable to resolve class GATKIntervalSummary
@ line 35, column 33.
GATKIntervalSummary summary = new GATKIntervalSummary(intervalFiles[sample].absolutePath)
^
/home/sark/ximmer/src/main/groovy/GATKMeanEstimator.groovy: 35: unable to resolve class GATKIntervalSummary
@ line 35, column 43.
GATKIntervalSummary summary = new GATKIn
^
/home/sark/ximmer/src/main/groovy/PositiveControlResults.groovy: 5: unable to resolve class gngs.RangedData
@ line 5, column 1.
import gngs.RangedData
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 8: unable to resolve class Cli
@ line 8, column 5.
Cli cli = new Cli(usage:"SimulateCNVs [options]\n")
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 8: unable to resolve class Cli
@ line 8, column 11.
Cli cli = new Cli(usage:"SimulateCNVs [options]\n")
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 50: unable to resolve class Pedigrees
@ line 50, column 15.
Pedigrees peds = Pedigrees.parse(opts.ped)
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 60: unable to resolve class Regions
@ line 60, column 9.
Regions excludeRegions = null
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 62: unable to resolve class DGV
@ line 62, column 9.
DGV dgv = new DGV(opts.dgv).parse()
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 62: unable to resolve class DGV
@ line 62, column 15.
DGV dgv = new DGV(opts.dgv).parse()
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 77: unable to resolve class Regions
@ line 77, column 7.
} as Regions
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 63: unable to resolve class Region
@ line 63, column 31.
excludeRegions = dgv.grep { Region cnv ->
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 99: unable to resolve class SAM
@ line 99, column 12.
bamFiles[new SAM(bam).samples[0]] = bam
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 124: unable to resolve class BED
@ line 124, column 9.
BED bed = new BED(opts.r).load()
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 124: unable to resolve class BED
@ line 124, column 15.
BED bed = new BED(opts.r).load()
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 125: unable to resolve class Regions
@ line 125, column 13.
Regions coveredRegions = new BED(opts.abed).load().reduce()
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 125: unable to resolve class BED
@ line 125, column 30.
Regions coveredRegions = new BED(opts.abed).load().reduce()
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 132: unable to resolve class Region
@ line 132, column 12.
Region r = simulator.selectRegion(bed, numRanges, excludeRegions)
^
/home/sark/ximmer/src/main/groovy/SimulateCNVs.groovy: 162: unable to resolve class SampleInfo
@ line 162, column 13.
new SampleInfo(sample: cnv.female, batch: new File(opts.d).name, target:"SIM", files: samples[cnv.female].files, sex: "FEMALE").toTsv()
^
/home/sark/ximmer/src/main/groovy/SimulationRun.groovy: 1: unable to resolve class gngs.SAM
@ line 1, column 1.
import gngs.SAM
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 5: unable to resolve class graxxia.Stats
@ line 5, column 1.
import graxxia.Stats
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 22: unable to resolve class RangedData
@ line 22, column 16.
Map<String,RangedData> results = [:]
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 27: unable to resolve class Regions
@ line 27, column 5.
Regions targetRegions
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 37: unable to resolve class VCF
@ line 37, column 10.
List<VCF> vcfs = []
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 47: unable to resolve class Regions
@ line 47, column 17.
Map<String, Regions> variants = [:]
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 51: unable to resolve class TargetedCNVAnnotator
@ line 51, column 5.
TargetedCNVAnnotator cnvAnnotator = null
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 53: unable to resolve class RefGenes
@ line 53, column 5.
RefGenes refGenes = null
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 94: unable to resolve class RangedData
@ line 94, column 93.
, Closure factory, Map<String,RangedData
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 108: unable to resolve class Cli
@ line 108, column 13.
Cli cli = new Cli(usage: "SummarizeCNVs <options>")
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 108: unable to resolve class Cli
@ line 108, column 19.
Cli cli = new Cli(usage: "SummarizeCNVs <options>")
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 151: unable to resolve class RangedData
@ line 151, column 20.
Map<String,RangedData> results = [:]
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 198: unable to resolve class VCF
@ line 198, column 14.
List<VCF> vcfList = parseVCFs(opts, results)
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 200: unable to resolve class Regions
@ line 200, column 17.
Regions target = new BED(opts.target, withExtra:true).load()
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 200: unable to resolve class BED
@ line 200, column 26.
Regions target = new BED(opts.target, withExtra:true).load()
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 206: unable to resolve class RefGenes
@ line 206, column 22.
RefGenes refGenes = (!opts.refgene || "download" == opts.refgene) ? RefGenes.download(opts.genome?:"hg19") : new RefGenes(opts.refgene)
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 206: unable to resolve class RefGenes
@ line 206, column 122.
wnload(opts.genome?:"hg19") : new RefGen
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 227: unable to resolve class TargetedCNVAnnotator
@ line 227, column 43.
summarizer.cnvAnnotator = new Target
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 235: unable to resolve class RefGenes
@ line 235, column 39.
summarizer.refGenes = new RefGenes(opts.refgene)
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 253: unable to resolve class Regions
@ line 253, column 21.
Regions cnvs = summarizer.run(exportSamples)
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 302: unable to resolve class RangedData
@ line 302, column 64.
tionAccessor opts, Map<String,RangedData
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 302: unable to resolve class VCF
@ line 302, column 17.
static List<VCF> parseVCFs(OptionAccessor opts, Map<String,RangedData> results) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 303: unable to resolve class Regions
@ line 303, column 17.
Regions mergedCalls = results*.value.inject(new Regions()) { Regions regions, RangedData calls ->
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 303: unable to resolve class Regions
@ line 303, column 53.
Calls = results*.value.inject(new Region
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 303: unable to resolve class Regions
@ line 303, column 68.
*.value.inject(new Regions()) { Regions
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 303: unable to resolve class RangedData
@ line 303, column 68.
*.value.inject(new Regions()) { Regions
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 308: unable to resolve class VCF
@ line 308, column 14.
List<VCF> vcfList = opts.vcfs ? opts.vcfs.collect {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 309: unable to resolve class Variant
@ line 309, column 27.
VCF.parse(it) { Variant v ->
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 329: unable to resolve class Regions
@ line 329, column 5.
Regions run(List exportSamples) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 335: unable to resolve class TargetedCNVAnnotator
@ line 335, column 33.
this.cnvAnnotator = new TargetedCNVAnnotator(targetRegions, dgvFile)
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 347: unable to resolve class Regions
@ line 347, column 17.
Regions results = new Regions()
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 347: unable to resolve class Regions
@ line 347, column 27.
Regions results = new Regions()
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 349: unable to resolve class Regions
@ line 349, column 21.
Regions sampleCnvs = extractSampleCnvs(s)
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 383: unable to resolve class Regions
@ line 383, column 23.
void metaAnnotate(Regions results) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 384: unable to resolve class Region
@ line 384, column 9.
for(Region cnv in results) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 394: unable to resolve class Regions
@ line 394, column 19.
void writeTSV(Regions cnvs, String fileName) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 404: unable to resolve class Region
@ line 404, column 39.
cnvAnnotator.annotate(new Region(cnv.chr, cnv.from..cnv.to), anno_types[cnv.type])
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 439: unable to resolve class Regions
@ line 439, column 20.
void writeJSON(Regions cnvs, String fileName) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 449: unable to resolve class Region
@ line 449, column 39.
cnvAnnotator.annotate(new Region(cnv.chr, cnv.from..cnv.to), anno_types[cnv.type])
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 496: unable to resolve class Regions
@ line 496, column 22.
void writeReport(Regions cnvs,
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 574: unable to resolve class Regions
@ line 574, column 5.
Regions extractSampleCnvs(String sample) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 577: unable to resolve class Regions
@ line 577, column 17.
Regions merged = new Regions()
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 577: unable to resolve class Regions
@ line 577, column 26.
Regions merged = new Regions()
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 579: unable to resolve class Region
@ line 579, column 13.
for(Region cnv in calls.grep { it.sample == sample }) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 584: unable to resolve class Regions
@ line 584, column 17.
Regions flattened = merged.reduce()
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 590: unable to resolve class Regions
@ line 590, column 17.
Regions result = new Regions()
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 590: unable to resolve class Regions
@ line 590, column 26.
Regions result = new Regions()
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 594: unable to resolve class Region
@ line 594, column 9.
for(Region cnv in flattened) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 603: unable to resolve class Region
@ line 603, column 9.
for(Region cnv in result) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 615: unable to resolve class Region
@ line 615, column 46.
iltered(List<String> callers, Region cnv
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 662: unable to resolve class Region
@ line 662, column 26.
def checkCallQuality(Region cnv, caller) {
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 686: unable to resolve class Region
@ line 686, column 51.
(String sample, List callers, Region cnv
^
/home/sark/ximmer/src/main/groovy/SummarizeCNVs.groovy: 691: unable to resolve class Region
@ line 691, column 20.
Region best = results[caller].grep { it.sample == sample && it.overlaps(cnv) }.max { it.quality?.toFloat() }
^
/home/sark/ximmer/src/main/groovy/SummaryReport.groovy: 127: unable to resolve class Region
@ line 127, column 14.
List<Region> cnvs = ximmer.readCnvs()
^
/home/sark/ximmer/src/main/groovy/SummaryReport.groovy: 130: unable to resolve class RangedData
@ line 130, column 14.
List<RangedData> results = ximmer.runs*.value*.runDirectory.collect { runDir ->
^
/home/sark/ximmer/src/main/groovy/SummaryReport.groovy: 131: unable to resolve class RangedData
@ line 131, column 13.
new RangedData(new File(runDir,"$analysisCfg.analysisName/report/cnv_report.tsv").path).load([:], { r ->
^
/home/sark/ximmer/src/main/groovy/SummaryReport.groovy: 161: unable to resolve class Region
@ line 161, column 37.
void plotCNVSizeHistograms(List<Region> cnvs) {
^
/home/sark/ximmer/src/main/groovy/SummaryReport.groovy: 172: unable to resolve class Region
@ line 172, column 36.
File writeCombinedCNVInfo(List<Region> cnvs) {
^
/home/sark/ximmer/src/main/groovy/XHMMResults.groovy: 4: unable to resolve class gngs.RangedData
@ line 4, column 1.
import gngs.RangedData
^
/home/sark/ximmer/src/main/groovy/XHMMResults.groovy: 5: unable to resolve class gngs.Region
@ line 5, column 1.
import gngs.Region
^
/home/sark/ximmer/src/main/groovy/XHMMResults.groovy: 2: unable to resolve class com.xlson.groovycsv.PropertyMapper
@ line 2, column 1.
import com.xlson.groovycsv.PropertyMapper
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 72: unable to resolve class SAM
@ line 72, column 17.
Map<String, SAM> bamFiles = [:]
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 74: unable to resolve class Pedigrees
@ line 74, column 5.
Pedigrees pedigrees = null
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 88: unable to resolve class Regions
@ line 88, column 5.
Regions targetRegion = null
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 90: unable to resolve class Regions
@ line 90, column 5.
Regions excludeRegions = null
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 100: unable to resolve class DGV
@ line 100, column 5.
DGV dgv
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 192: unable to resolve class BED
@ line 192, column 29.
this.targetRegion = new BED(cfg.target_regions).load().reduce()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 265: unable to resolve class DGV
@ line 265, column 15.
dgv = new DGV(dgvMergedFile.absolutePath).parse()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 655: unable to resolve class Pedigrees
@ line 655, column 26.
this.pedigrees = new Pedigrees()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 660: unable to resolve class Pedigrees
@ line 660, column 23.
Pedigrees males = Pedigrees.fromSingletons(cfg.samples.males)
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 666: unable to resolve class Pedigrees
@ line 666, column 23.
Pedigrees females = Pedigrees.fromSingletons(cfg.samples.females)
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 682: unable to resolve class SexKaryotyper
@ line 682, column 14.
List<SexKaryotyper> unknownResults = []
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 684: unable to resolve class SAM
@ line 684, column 9.
for(SAM sam in this.bamFiles*.value) {
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 686: unable to resolve class SexKaryotyper
@ line 686, column 27.
SexKaryotyper typer = new SexKaryotyper(sam, this.targetRegion)
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 686: unable to resolve class SexKaryotyper
@ line 686, column 35.
SexKaryotyper typer = new SexKaryotyper(sam, this.targetRegion)
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 715: unable to resolve class Region
@ line 715, column 10.
List<Region> simulateRun(String runId) {
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 747: unable to resolve class SAM
@ line 747, column 14.
List<SAM> existingBams = Files.newDirectoryStream(bamDir.toPath(), '*.bam').grep { Path p ->
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 750: unable to resolve class SAM
@ line 750, column 31.
}.collect { Path p -> new SAM(p.toFile()) }
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 755: unable to resolve class SAM
@ line 755, column 14.
List<SAM> targetSamples = computeTargetSamples()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 756: unable to resolve class Region
@ line 756, column 14.
List<Region> simulatedCNVs = []
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 759: unable to resolve class Regions
@ line 759, column 17.
Regions initialExclusions = this.excludeRegions ? this.excludeRegions.collect { it } as Regions : new Regions()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 759: unable to resolve class Regions
@ line 759, column 94.
excludeRegions.collect { it } as Regions
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 759: unable to resolve class Regions
@ line 759, column 107.
s.collect { it } as Regions : new Region
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 780: unable to resolve class Region
@ line 780, column 47.
VFile(File trueCnvsFile, List<Region> si
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 807: unable to resolve class RangedData
@ line 807, column 20.
RangedData cnvs = new RangedData(knownCnvsFile).load(columnNames: ['chr','start','end','sample','type'])
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 807: unable to resolve class RangedData
@ line 807, column 27.
RangedData cnvs = new RangedData(knownCnvsFile).load(columnNames: ['chr','start','end','sample','type'])
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 814: unable to resolve class SAM
@ line 814, column 103.
String> existingSamples, List<SAM> exist
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 814: unable to resolve class SAM
@ line 814, column 122.
ples, List<SAM> existingBams, SAM target
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 814: unable to resolve class Regions
@ line 814, column 5.
Regions simulateSampleCNVs(Exclusions exclusions, File bamDir, List<String> existingSamples, List<SAM> existingBams, SAM targetSAM) {
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 817: unable to resolve class Regions
@ line 817, column 21.
Regions cnvs = checkExistingSimulatedSample(bamDir, existingSamples, existingBams, sample)
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 848: unable to resolve class Regions
@ line 848, column 5.
Regions checkExistingSimulatedSample(File outputDir, List existingSamples, List existingBams, String sample) {
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 855: unable to resolve class SAM
@ line 855, column 13.
SAM existingSAM = existingBams[existingIndex]
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 864: unable to resolve class Regions
@ line 864, column 17.
Regions result = new Regions()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 864: unable to resolve class Regions
@ line 864, column 26.
Regions result = new Regions()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 866: unable to resolve class Regions
@ line 866, column 17.
Regions cnvs = new BED(bedFile).load()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 866: unable to resolve class BED
@ line 866, column 24.
Regions cnvs = new BED(bedFile).load()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 881: unable to resolve class SAM
@ line 881, column 71.
s exclusions, File outputDir, SAM target
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 881: unable to resolve class Regions
@ line 881, column 5.
Regions simulateSampleCNVs(Exclusions exclusions, File outputDir, SAM targetSample) {
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 886: unable to resolve class SAM
@ line 886, column 13.
SAM sourceSample = null
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 899: unable to resolve class Regions
@ line 899, column 17.
Regions deletions = selectSampleCNVRegions(exclusions, targetSample, sourceSample)
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 902: unable to resolve class Region
@ line 902, column 16.
Region r = deletions[0]
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 940: unable to resolve class SAM
@ line 940, column 59.
egions(Exclusions exclusions, SAM target
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 940: unable to resolve class SAM
@ line 940, column 77.
exclusions, SAM targetSample, SAM source
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 940: unable to resolve class Regions
@ line 940, column 5.
Regions selectSampleCNVRegions(Exclusions exclusions, SAM targetSample, SAM sourceSample) {
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 944: unable to resolve class Regions
@ line 944, column 17.
Regions simulationRegions = this.targetRegion
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 946: unable to resolve class Regions
@ line 946, column 33.
simulationRegions = new Regions(this.targetRegion.grep { it.chr == 'chrX' || it.chr == 'X' })
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 949: unable to resolve class Regions
@ line 949, column 17.
Regions deletions = new Regions()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 949: unable to resolve class Regions
@ line 949, column 29.
Regions deletions = new Regions()
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 951: unable to resolve class Region
@ line 951, column 20.
Region r = selectSampleCNVRegion(exclusions, cnvIndex, simulationRegions, targetSample, sourceSample)
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 960: unable to resolve class Regions
@ line 960, column 68.
usions exclusions, int cnvId, Regions si
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 960: unable to resolve class SAM
@ line 960, column 95.
d, Regions simulationRegions, SAM target
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 960: unable to resolve class SAM
@ line 960, column 113.
ionRegions, SAM targetSample, SAM source
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 960: unable to resolve class Region
@ line 960, column 5.
Region selectSampleCNVRegion(Exclusions exclusions, int cnvId, Regions simulationRegions, SAM targetSample, SAM sourceSample) {
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 977: unable to resolve class Region
@ line 977, column 16.
Region selectedRegion = Utils.withRetries(REGION_SIZE_SELECTION_RETRIES, message: "Select deletion region for $sampleId") {
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 989: unable to resolve class Region
@ line 989, column 20.
Region r = simulator.selectRegion(simulationRegions, numRegions, exclusions)
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1007: unable to resolve class SAM
@ line 1007, column 10.
List<SAM> computeTargetSamples() {
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1022: unable to resolve class SAM
@ line 1022, column 18.
List<SAM> results = this.bamFiles.grep { Map.Entry e ->
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1078: unable to resolve class Region
@ line 1078, column 10.
List<Region> readCnvs() {
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1079: unable to resolve class Region
@ line 1079, column 14.
List<Region> cnvs = []
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1083: unable to resolve class Region
@ line 1083, column 61.
e,withExtra:true).load().each { Region r
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1083: unable to resolve class BED
@ line 1083, column 17.
new BED(cnvFile,withExtra:true).load().each { Region r ->
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1092: unable to resolve class Region
@ line 1092, column 19.
cnvs.each { Region r ->
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1237: unable to resolve class Cli
@ line 1237, column 13.
Cli cli = new Cli(usage:"ximmer -c <config> -o <output_directory>")
^
/home/sark/ximmer/src/main/groovy/Ximmer.groovy: 1237: unable to resolve class Cli
@ line 1237, column 19.
Cli cli = new Cli(usage:"ximmer -c <config> -o <output_directory>")
^
/home/sark/ximmer/src/main/groovy/ximmer/Exclusions.groovy: 5: unable to resolve class gngs.Region
@ line 5, column 1.
import gngs.Region
^
/home/sark/ximmer/src/main/groovy/ximmer/Exclusions.groovy: 6: unable to resolve class gngs.Regions
@ line 6, column 1.
import gngs.Regions
^
310 errors
ssadedin
bopohdr
Im running the analysis on 14 BAM files 7 from tumor and 7 from its germline. which is in a /mnt/d/AKU/FTP/BAM/.
I rand the following command to test the tool:
./ximmer -v -nosim -c /mnt/d/AKU/FTP/BAM/config.groovy -o resultsThis is my config.groovy file:
After Running im getting the following error:
While installing XIMMER i was unable to install xhmm only all other were success and i was also unable to solve the xhmm error which is:
Can you please help?