polish help info

medvedevgroup · Jun 22, 2018 · 1c3ad5a · 1c3ad5a
1 parent 91479cc
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diff --git a/experiment/experiment.md b/experiment/experiment.md
@@ -36,13 +36,13 @@ mv SNPs142_hg19_Common.filt.txt snp.txt
 
 1. generate index files `ref.dict`, `snp.dict`, `ref.bf` and `snp.bf` and also chrlens file `ref.fa.chrlens`
 
-```$VARGENO/vargeno index hg19.fa snp.txt exp.idx```
+```$VARGENO/vargeno index hg19.fa snp.txt experiment```
 
 # Genotyping
 
 ## Using VarGeno
 
-```$VARGENO/vargeno geno exp.idx reads.fq ref.fa.chrlens genotype.out```
+```$VARGENO/vargeno geno experiment reads.fq ref.fa.chrlens genotype.out```
 > **Do not forget the command `geno` after `vargeno`**
 
 # Other data

diff --git a/src/qv.cc b/src/qv.cc
@@ -1831,16 +1831,16 @@ static void print_help(void)
 	fprintf(stderr, "Usage: vargeno <option> [option parameters ...]\n");
 	fprintf(stderr, "Option  Description                   Parameters\n");
 	fprintf(stderr, "------  -----------                   ----------\n");
-	fprintf(stderr, "ucscd    Generate dictionary files, if known SNPs are in UCSC text file format     "
-	                "<input FASTA> <input SNPs> <output ref dict> <output SNP dict>\n");
-	fprintf(stderr, "vcfd    Generate dictionary files, if known SNPs are in VCF file format    "
-	                "<input FASTA> <input SNPs> <output ref dict> <output SNP dict>\n");
-	fprintf(stderr, "ucscbf    Generate Bloom filter files, if known SNPs are in UCSC text file format     "
-	                "<input FASTA> <input SNPs> <output ref bloom filter> <output SNP bloom filter>\n");
-	fprintf(stderr, "vcfbf    Generate dictionary files, if known SNPs are in VCF file format    "
-	                "<input FASTA> <input SNPs> <output ref bloom filter> <output SNP bloom filter>\n");
-	fprintf(stderr, "genotype    Perform genotyping            "
-	                "<input ref dict> <input SNP dict> <input FASTQ> <chrlens file> <ref Bloom filter> <snp Bloom filter> <output file>\n");
+	//fprintf(stderr, "ucscd    Generate dictionary files, if known SNPs are in UCSC text file format     "
+	//                "<input FASTA> <input SNPs> <output ref dict> <output SNP dict>\n");
+	//fprintf(stderr, "vcfd    Generate dictionary files, if known SNPs are in VCF file format    "
+	//                "<input FASTA> <input SNPs> <output ref dict> <output SNP dict>\n");
+	//fprintf(stderr, "ucscbf    Generate Bloom filter files, if known SNPs are in UCSC text file format     "
+	//                "<input FASTA> <input SNPs> <output ref bloom filter> <output SNP bloom filter>\n");
+	//fprintf(stderr, "vcfbf    Generate dictionary files, if known SNPs are in VCF file format    "
+	//                "<input FASTA> <input SNPs> <output ref bloom filter> <output SNP bloom filter>\n");
+	//fprintf(stderr, "genotype    Perform genotyping            "
+	//                "<input ref dict> <input SNP dict> <input FASTQ> <chrlens file> <ref Bloom filter> <snp Bloom filter> <output file>\n");
 
 	fprintf(stderr, "index   Generate index            "
 	                "<input FASTA> <input SNPs> <index_prefix>\n");