cram input

[GSBaohuaGu]

I tried the method you mentioned solve the problem if the input is cram format, but still reported an error.
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/compress/compressors/bzip2/BZip2CompressorOutputStream
at htsjdk.samtools.cram.structure.block.Block.getUncompressedContent(Block.java:203)
at htsjdk.samtools.cram.build.CramIO.readSAMFileHeader(CramIO.java:316)
at htsjdk.samtools.cram.build.CramIO.readCramHeader(CramIO.java:225)
at htsjdk.samtools.cram.build.CramContainerIterator.(CramContainerIterator.java:22)
at htsjdk.samtools.CRAMIterator.(CRAMIterator.java:86)
at htsjdk.samtools.CRAMFileReader.initWithStreams(CRAMFileReader.java:226)
at htsjdk.samtools.CRAMFileReader.(CRAMFileReader.java:219)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:422)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:208)
at com.astrazeneca.vardict.VarDictLauncher.readChr(VarDictLauncher.java:187)
at com.astrazeneca.vardict.VarDictLauncher.initResources(VarDictLauncher.java:80)
at com.astrazeneca.vardict.VarDictLauncher.start(VarDictLauncher.java:49)
at com.astrazeneca.vardict.Main.main(Main.java:15)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
... 13 more

[karlestira]

you can download a new htsjdk and build it with full dependency addon (using IntelliJ IDEA to build with command ./gradlew shadowJar, the zip file is htsjdk 3.0.5), and use CLASSPATH=[htsjdk.jar]:[vardict.jar] (notice the order is important) when launch JVM. This will replace htsjdk in vardict with your new htsjdk and fix dependency problem.

java -classpath "[path of htsjdk.jar]:[path of vardict.jar]" com.astrazeneca.vardict.Main [other vardict params]

htsjdk-3.0.5.jar.zip

however, Vardict will be greatly slower(2 times or more depend on the seqs_per_slice set when generate CRAM) when runing on CRAM. Your CRAM is compressed in bzip2 format so the seqs_per_slice is very high by default in samtools(which means Vardict will be very very slow). If possible, I suggest converting your CRAM to BAM.