Add more CLI validation

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala

@@ -208,8 +208,12 @@ object ExtractAlignedFastq extends ToolCommand {
         |This tool creates FASTQ file(s) containing reads mapped to the given alignment intervals.
       """.stripMargin)
 
-    checkConfig { c=>
-      if (c.inputFastq2 != null && c.outputFastq2 == null)
+    checkConfig { c =>
+      if (!c.inputBam.exists)
+        failure("Input BAM file not found")
+      else if (!c.inputFastq1.exists)
+        failure("Input FASTQ file 1 not found")
+      else if (c.inputFastq2 != null && c.outputFastq2 == null)
         failure("Missing output FASTQ file 2")
       else if (c.inputFastq2 == null && c.outputFastq2 != null)
         failure("Missing input FASTQ file 2")