Option -i is missing from Options: long text

[tseemann]

-i is in Usage: but it is not in Options:

Usage: ../MapCaller -i Index_Prefix -f <ReadFile_A1 ReadFile_B1 ...> [-f2 <ReadFile_A2 ReadFile_B2 ...>]

Options: -t INT        number of threads [16]
         -f            files with #1 mates reads (format:fa, fq, fq.gz)
         -f2           files with #2 mates reads (format:fa, fq, fq.gz)
         -size         Sequncing fragment size [500]
         -ad INT       Minimal ALT allele count [10]
         -sam          SAM output filename [NULL]
         -bam          BAM output filename [NULL]
         -vcf          VCF output filename [output.vcf]
         -m            output multiple alignments
         -somatic      detect somatic mutations [false]
         -no_vcf       No VCF output [false]
         -p            paired-end reads are interlaced in the same file
         -filter       apply variant filters (under test) [false]
         -v            version

[hsinnan75]

fixed it! thanks!