diff --git a/README.md b/README.md index b06a8ee..c1e4f05 100644 --- a/README.md +++ b/README.md @@ -74,8 +74,7 @@ A standard VCF can be used as a mutation file, with file extension `.vcf` or `.V ```shell mutscan -1 R1.fq -2 R2.fq -m target.vcf -r hg19.fa -h report.html ``` -* if the VCF file is smaller than 100 records, all records can be scanned -* if the VCF file has more than 100 records, you should add `--mark` in the command line, and then mark the wanted records with the `FILTER` column marked `M`. For example (note the M in the FILTER column): +* if the VCF file has too many records, you will get a very big HTML file if you scan all the variants. You can add `--mark` in the command line, and then mark the wanted records with the `FILTER` column marked `M`. For example (note the M in the FILTER column): ``` #CHROM POS ID REF ALT QUAL FILTER INFO 1 69224 COSM3677745 A C . M This record will be scanned diff --git a/src/common.h b/src/common.h index 5aedaa3..a570ceb 100644 --- a/src/common.h +++ b/src/common.h @@ -1,7 +1,7 @@ #ifndef COMMON_H #define COMMON_H -#define MUTSCAN_VER "1.8.0" +#define MUTSCAN_VER "1.9.0" typedef long int64; typedef unsigned long uint64; diff --git a/src/mutation.cpp b/src/mutation.cpp index e812caa..eee76d3 100644 --- a/src/mutation.cpp +++ b/src/mutation.cpp @@ -246,7 +246,7 @@ vector Mutation::parseVcf(string vcfFile, string refFile) { mutations.push_back(mut); } if(mutations.size() <= 0){ - cerr<<"No mutation will be scanned"<