diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala index 1ec41952922c2058d02f680efb8a14a1757c85a2..710d24ac931b65aa1d020cd691f219ffe4ac6aed 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala @@ -317,6 +317,8 @@ object SeqStat extends ToolCommand { )) ) + // TODO: have function generate map so that it can be tested + println(ConfigUtils.mapToJson(report)) } } diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala index d9180aec45025b68e9830227110ca9320571b683..c9dd5e290c3cd4da97c58198da2a596258ed0c64 100644 --- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala +++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala @@ -101,4 +101,6 @@ class SeqStatTest extends TestNGSuite with MockitoSugar with Matchers { val parsed = parseArgs(args) parsed.fastq shouldBe resourceFile("/paired01a.fq") } + + // TODO: Shared state here. Calling main changes the state, which causes other tests to fail } \ No newline at end of file