Add mutational signatures for cancer types

colorectal cancer, lung adenmocarcinoma, melanoma, and stomach cancer.

Also update the version to Osprey 3.3

build.gradle.kts

@@ -59,7 +59,7 @@ group = "edu.duke.cs"
  * This version number is largely cosmetic, compared to the versioning scheme for the Osprey Service
  * But it does help users provide some information to developers when reporting issues.
  */
-version = "4.0.2"
+version = "3.3"
 
 repositories {
 	mavenCentral()
@@ -224,7 +224,8 @@ tasks.withType<Test> {
 	maxHeapSize = "2g"
 	useJUnit()
     failFast = true
-	Jvm.addModuleArgs(jvmArgs)
+	// method call appends additional arguments for the JVM
+	jvmArgs(Jvm.moduleArgs)
 
 	testLogging {
 		setExceptionFormat("full")

src/main/julia/resistor/mutational-signatures/colorectal_cancer.json

@@ -0,0 +1,322 @@
+{
+   "AAA" : {
+      "ACA" : 0.002251402,
+      "AGA" : 0.003883608,
+      "ATA" : 0.000961065
+   },
+   "AAC" : {
+      "ACC" : 0.000601336,
+      "AGC" : 0.005198815,
+      "ATC" : 0.000504114
+   },
+   "AAG" : {
+      "ACG" : 0.001820715,
+      "AGG" : 0.006886609,
+      "ATG" : 0.001049023
+   },
+   "AAT" : {
+      "ACT" : 0.000835687,
+      "AGT" : 0.005694241,
+      "ATT" : 0.001679238
+   },
+   "ACA" : {
+      "AAA" : 0.001708509,
+      "AGA" : 0.000828116,
+      "ATA" : 0.006498599
+   },
+   "ACC" : {
+      "AAC" : 0.001661245,
+      "AGC" : 0.000727878,
+      "ATC" : 0.003818251
+   },
+   "ACG" : {
+      "AAG" : 0.000264205,
+      "AGG" : 0.000158004,
+      "ATG" : 0.015854537
+   },
+   "ACT" : {
+      "AAT" : 0.001263405,
+      "AGT" : 0.000949,
+      "ATT" : 0.003958479
+   },
+   "AGA" : {
+      "AAA" : 0.004413345,
+      "ACA" : 0.00114861,
+      "ATA" : 0.005792534
+   },
+   "AGC" : {
+      "AAC" : 0.007210625,
+      "ACC" : 0.0006307,
+      "ATC" : 0.001896027
+   },
+   "AGG" : {
+      "AAG" : 0.003954967,
+      "ACG" : 0.000572839,
+      "ATG" : 0.006014902
+   },
+   "AGT" : {
+      "AAT" : 0.003958479,
+      "ACT" : 0.000949,
+      "ATT" : 0.001263405
+   },
+   "ATA" : {
+      "AAA" : 0.000777486,
+      "ACA" : 0.005692943,
+      "AGA" : 0.000136402
+   },
+   "ATC" : {
+      "AAC" : 0.001909194,
+      "ACC" : 0.004232849,
+      "AGC" : 0.000316299
+   },
+   "ATG" : {
+      "AAG" : 0.00107702,
+      "ACG" : 0.005555689,
+      "AGG" : 0.000627456
+   },
+   "ATT" : {
+      "AAT" : 0.001679238,
+      "ACT" : 0.005694241,
+      "AGT" : 0.000835687
+   },
+   "CAA" : {
+      "CCA" : 0.000524509,
+      "CGA" : 0.002944184,
+      "CTA" : 0.000326501
+   },
+   "CAC" : {
+      "CCC" : 0.000756944,
+      "CGC" : 0.003891829,
+      "CTC" : 0.000420948
+   },
+   "CAG" : {
+      "CCG" : 0.000896579,
+      "CGG" : 0.005946786,
+      "CTG" : 0.000633509
+   },
+   "CAT" : {
+      "CCT" : 0.000627456,
+      "CGT" : 0.005555689,
+      "CTT" : 0.00107702
+   },
+   "CCA" : {
+      "CAA" : 0.002691811,
+      "CGA" : 0.000300167,
+      "CTA" : 0.005243752
+   },
+   "CCC" : {
+      "CAC" : 0.002736404,
+      "CGC" : 0.000422373,
+      "CTC" : 0.003786673
+   },
+   "CCG" : {
+      "CAG" : 0.001058204,
+      "CGG" : 0.000162736,
+      "CTG" : 0.012987556
+   },
+   "CCT" : {
+      "CAT" : 0.006014902,
+      "CGT" : 0.000572839,
+      "CTT" : 0.003954967
+   },
+   "CGA" : {
+      "CAA" : 0.009956757,
+      "CCA" : 0.000110068,
+      "CTA" : 0.000673967
+   },
+   "CGC" : {
+      "CAC" : 0.0165884,
+      "CCC" : 2.6334e-05,
+      "CTC" : 0.000372331
+   },
+   "CGG" : {
+      "CAG" : 0.012987556,
+      "CCG" : 0.000162736,
+      "CTG" : 0.001058204
+   },
+   "CGT" : {
+      "CAT" : 0.015854537,
+      "CCT" : 0.000158004,
+      "CTT" : 0.000264205
+   },
+   "CTA" : {
+      "CAA" : 0.000390422,
+      "CCA" : 0.002568071,
+      "CGA" : 0.000145181
+   },
+   "CTC" : {
+      "CAC" : 0.000927223,
+      "CCC" : 0.005547155,
+      "CGC" : 0.000697439
+   },
+   "CTG" : {
+      "CAG" : 0.000633509,
+      "CCG" : 0.005946786,
+      "CGG" : 0.000896579
+   },
+   "CTT" : {
+      "CAT" : 0.001049023,
+      "CCT" : 0.006886609,
+      "CGT" : 0.001820715
+   },
+   "GAA" : {
+      "GCA" : 0.000728493,
+      "GGA" : 0.004281007,
+      "GTA" : 0.000993413
+   },
+   "GAC" : {
+      "GCC" : 0.000258255,
+      "GGC" : 0.004551004,
+      "GTC" : 0.000648729
+   },
+   "GAG" : {
+      "GCG" : 0.000697439,
+      "GGG" : 0.005547155,
+      "GTG" : 0.000927223
+   },
+   "GAT" : {
+      "GCT" : 0.000316299,
+      "GGT" : 0.004232849,
+      "GTT" : 0.001909194
+   },
+   "GCA" : {
+      "GAA" : 0.002754393,
+      "GGA" : 0.000307573,
+      "GTA" : 0.008430829
+   },
+   "GCC" : {
+      "GAC" : 0.001469207,
+      "GGC" : 0.000641657,
+      "GTC" : 0.009348964
+   },
+   "GCG" : {
+      "GAG" : 0.000372331,
+      "GGG" : 2.6334e-05,
+      "GTG" : 0.0165884
+   },
+   "GCT" : {
+      "GAT" : 0.001896027,
+      "GGT" : 0.0006307,
+      "GTT" : 0.007210625
+   },
+   "GGA" : {
+      "GAA" : 0.004354559,
+      "GCA" : 0.00060226,
+      "GTA" : 0.002206242
+   },
+   "GGC" : {
+      "GAC" : 0.009348964,
+      "GCC" : 0.000641657,
+      "GTC" : 0.001469207
+   },
+   "GGG" : {
+      "GAG" : 0.003786673,
+      "GCG" : 0.000422373,
+      "GTG" : 0.002736404
+   },
+   "GGT" : {
+      "GAT" : 0.003818251,
+      "GCT" : 0.000727878,
+      "GTT" : 0.001661245
+   },
+   "GTA" : {
+      "GAA" : 0.000512491,
+      "GCA" : 0.00352488,
+      "GGA" : 6.5835e-05
+   },
+   "GTC" : {
+      "GAC" : 0.000648729,
+      "GCC" : 0.004551004,
+      "GGC" : 0.000258255
+   },
+   "GTG" : {
+      "GAG" : 0.000420948,
+      "GCG" : 0.003891829,
+      "GGG" : 0.000756944
+   },
+   "GTT" : {
+      "GAT" : 0.000504114,
+      "GCT" : 0.005198815,
+      "GGT" : 0.000601336
+   },
+   "TAA" : {
+      "TCA" : 0.000261637,
+      "TGA" : 0.002018701,
+      "TTA" : 0.000806968
+   },
+   "TAC" : {
+      "TCC" : 6.5835e-05,
+      "TGC" : 0.00352488,
+      "TTC" : 0.000512491
+   },
+   "TAG" : {
+      "TCG" : 0.000145181,
+      "TGG" : 0.002568071,
+      "TTG" : 0.000390422
+   },
+   "TAT" : {
+      "TCT" : 0.000136402,
+      "TGT" : 0.005692943,
+      "TTT" : 0.000777486
+   },
+   "TCA" : {
+      "TAA" : 0.00279994,
+      "TGA" : 0.000395836,
+      "TTA" : 0.004466346
+   },
+   "TCC" : {
+      "TAC" : 0.002206242,
+      "TGC" : 0.00060226,
+      "TTC" : 0.004354559
+   },
+   "TCG" : {
+      "TAG" : 0.000673967,
+      "TGG" : 0.000110068,
+      "TTG" : 0.009956757
+   },
+   "TCT" : {
+      "TAT" : 0.005792534,
+      "TGT" : 0.00114861,
+      "TTT" : 0.004413345
+   },
+   "TGA" : {
+      "TAA" : 0.004466346,
+      "TCA" : 0.000395836,
+      "TTA" : 0.00279994
+   },
+   "TGC" : {
+      "TAC" : 0.008430829,
+      "TCC" : 0.000307573,
+      "TTC" : 0.002754393
+   },
+   "TGG" : {
+      "TAG" : 0.005243752,
+      "TCG" : 0.000300167,
+      "TTG" : 0.002691811
+   },
+   "TGT" : {
+      "TAT" : 0.006498599,
+      "TCT" : 0.000828116,
+      "TTT" : 0.001708509
+   },
+   "TTA" : {
+      "TAA" : 0.000806968,
+      "TCA" : 0.002018701,
+      "TGA" : 0.000261637
+   },
+   "TTC" : {
+      "TAC" : 0.000993413,
+      "TCC" : 0.004281007,
+      "TGC" : 0.000728493
+   },
+   "TTG" : {
+      "TAG" : 0.000326501,
+      "TCG" : 0.002944184,
+      "TGG" : 0.000524509
+   },
+   "TTT" : {
+      "TAT" : 0.000961065,
+      "TCT" : 0.003883608,
+      "TGT" : 0.002251402
+   }
+}