Update README.md

README.md

@@ -14,6 +14,7 @@ Run "make" in the program directory to compile
 --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
@@ -30,6 +31,7 @@ Run "make" in the program directory to compile
 --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