Run "make" in the program directory to compile
[REQUIRED ARGUMENTS]
--fasta <string> Input reference sequence file
--bam <string> Input bam file, in the format of SAMPLE_NAME:BAM_FILE. This paramter need to be specified at least once
e.g: --bam s_EV_crc_007:Proj_4495.eta_indelRealigned_recal_s_EV_crc_007_M3.bam.
--bam_fof <string> Input file of file with each row in the format of \"SAMPLE_NAME\tBAM_FILE\". This paramter is optional if --bam is specified at least once
--maf <string> Input variant file in TCGA maf format. --maf or --vcf need to be specified at least once. But --maf and --vcf are mutually exclusive
--vcf <string> Input variant file in vcf-like format(the first 5 columns are used). --maf or --vcf need to be specified at least once. But --maf and --vcf are mutually
--output <string> Output file
[OPTIONAL ARGUMENTS]
--omaf Output the result in maf format
--thread <int> Number of thread. Default 1
--maq <int> Mapping quality threshold. Default 20
--baq <int> Base quality threshold, Default 0
--filter_duplicate [0, 1] Whether to filter reads that are marked as duplicate. 0=off, 1=on. Default 1
--filter_improper_pair [0, 1] Whether to filter reads that are marked as improperly paired. 0=off, 1=on. Default 0
--filter_qc_failed [0, 1] Whether to filter reads that are marked as failed quality control. 0=off, 1=on. Default 0
--filter_indel [0, 1] Whether to filter reads that contain indels. 0=off, 1=on. Default 0
--filter_non_primary [0, 1] Whether to filter reads that are marked as non primary alignment. Default 0
--positive_count [0, 1] Whether to output positive strand read counts DPP/RDP/ADP. 0=off, 1=on. Default 1
--fragment_count [0, 1] Whether to output fragment read counts DPF/RDF/ADF. 0=off, 1=on. Default 0
--fragment_fractional_weight Whether to add a fractional depth (0.5) when there is disaggrement between strands on an ALT allele. Default 0
--suppress_warning <int> Only print a limit number of warnings for each type. Default 3
--help Print command line usage
[ADVANCED ARGUMENTS, CHANGING THESE ARGUMENTS MAY SIGNIFICANTLY AFFECT MEMORY USAGE AND RUNNING TIME. USE WITH CAUTION]
--max_block_size <int> The maximum number of variant chunks that can be processed at once per thread. Default 10,000
--max_block_dist <int> The longest spanning region (bp) of variant chunks that can be processed at once per thread. Default 100,000
--generic_counting Use the newly implemented generic counting algorithm. Works better for complex variants. You may get different allele count result from the default counting algorithm
### FAQ:
### This software uses the following library
bamtools https://github.com/pezmaster31/bamtools