input format issue on qbasepileup indel mode

[ChristinaXu2017]

Describe the bug There was a option to specify the snp position file format and output format. --is <somatic_indel_file> Path to somatic indel file and --ig <germline_file> Path to somatic indel file and --pindel adjust insertion position to conform to pindel format and --gatk adjust insertion position to conform to gatk format and --strelka adjust insertion position to conform to strelka format (same as pindel)

here pindel is a deprecated tool, so i tried gatk or strelka vcf files as input, eg. --is <strelka vcf> --strelka ... or --ig <gatk vcf> --gatk ... but get same exception: 23:06:04.863 [main] INFO org.qcmg.qbasepileup.indel.IndelBasePileupMT - org.qcmg.qbasepileup.QBasePileupException: Could not determine the type of the DCC header. Not sure of the QCMGFlag column at org.qcmg.qbasepileup.QBasePileupUtil.parseDCCHeader(QBasePileupUtil.java:140)

To Reproduce 'java -jar $jar --log $output.log -m indel --strelka --is $somaticIndel --it $input_bam --og $output -r $reference -in $input_bam'

Expected behavior indel mode should be deprecated, it seems only support dcc1 format which was our QCMG internal file and deprecated now.

Desktop (please complete the following information):

• OS: mac or linux
• Version : adamajava version 98-0412007c

Additional context Add any other context about the problem here.