VTC Not Working on Ion Torrent VCF Files

[drmrgd]

Hi, Have run into a NumberFormatException running Ion Torrent VCF files. Neither the supplied test VCF (TSVC_variants.vcf.gz) nor any of my own work, and I get the same error:

$ vtc VS -s I -i TSVC_variants.vcf.gz
2016-05-09 08:27:34 INFO  VarStatsEngine:91 - Namespace(SUMMARY=I, OUTPUT=null, pheno=null, VCF=[TSVC_variants.vcf.gz], association=false, DETAILED=null)
2016-05-09 08:27:34 INFO  AbstractVariantPool:135 - Opening TSVC_variants.vcf.gz for reading...
2016-05-09 08:27:34 INFO  AbstractVariantPool:211 - Setting samples
2016-05-09 08:27:34 ERROR VarStatsEngine:184 - Caught unexpected exception, something is very wrong!
java.lang.NumberFormatException: Infinite or NaN
    at java.math.BigDecimal.<init>(BigDecimal.java:895)
    at java.math.BigDecimal.<init>(BigDecimal.java:872)
    at vtc.tools.utilitybelt.UtilityBelt.round(UtilityBelt.java:57)
    at vtc.tools.varstats.VariantPoolSummarizer.getPercents(VariantPoolSummarizer.java:340)
    at vtc.tools.varstats.VariantPoolSummarizer.summarizeVariantPool(VariantPoolSummarizer.java:226)
    at vtc.tools.varstats.VariantPoolSummarizer.summarizeVariantPools(VariantPoolSummarizer.java:178)
    at vtc.tools.varstats.VarStatsEngine.doStats(VarStatsEngine.java:146)
    at vtc.VTCEngine.main(VTCEngine.java:66)

The other test VCFs work fine, and so I think this is strictly related to this particular dataset. I did re-install / re-compile the package with unit tests turned on, and all passed except for the VarStatsTest:

Test set: vtc.tools.varstats.VarStatsTest
-------------------------------------------------------------------------------
Tests run: 7, Failures: 3, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec <<< FAILURE! - in vtc.tools.varstats.VarStatsTest
testIndDetailedCombinedSummaryOneFile(vtc.tools.varstats.VarStatsTest)  Time elapsed: 0.007 sec  <<< FAILURE!
java.lang.AssertionError: null
        at org.junit.Assert.fail(Assert.java:86)
        at org.junit.Assert.assertTrue(Assert.java:41)
        at org.junit.Assert.assertTrue(Assert.java:52)
        at vtc.tools.varstats.VarStatsTest.Compare2DetailedSummaryFiles(VarStatsTest.java:438)
        at vtc.tools.varstats.VarStatsTest.testIndDetailedCombinedSummaryOneFile(VarStatsTest.java:392)

testCombinedSummary2Files(vtc.tools.varstats.VarStatsTest)  Time elapsed: 0.008 sec  <<< FAILURE!
java.lang.AssertionError: null
        at org.junit.Assert.fail(Assert.java:86)
        at org.junit.Assert.assertTrue(Assert.java:41)
        at org.junit.Assert.assertTrue(Assert.java:52)
        at vtc.tools.varstats.VarStatsTest.Compare2DetailedSummaryFiles(VarStatsTest.java:438)
        at vtc.tools.varstats.VarStatsTest.testCombinedSummary2Files(VarStatsTest.java:424)

testIndDetailedSummary(vtc.tools.varstats.VarStatsTest)  Time elapsed: 0.012 sec  <<< FAILURE!
java.lang.AssertionError: null
        at org.junit.Assert.fail(Assert.java:86)
        at org.junit.Assert.assertTrue(Assert.java:41)
        at org.junit.Assert.assertTrue(Assert.java:52)
        at vtc.tools.varstats.VarStatsTest.Compare2DetailedSummaryFiles(VarStatsTest.java:438)
        at vtc.tools.varstats.VarStatsTest.testIndDetailedSummary(VarStatsTest.java:361)

So, might be some issue with that particular component? Not sure what other info I can provide, but happy to help where possible.