修改参数顺序

run-featurecounts.R

@@ -11,10 +11,10 @@ p <- arg_parser("Run featureCounts and calculate FPKM/TPM")
 
 # 添加参数
 p <- add_argument(p, "--bam", help="input: bam file", type="character")
+p <- add_argument(p, "--strandSpecific", help="Strand specificity (0, 1, 2)", type="numeric", default=0)
 p <- add_argument(p, "--gtf", help="input: gtf file", type="character", default=NA)
 p <- add_argument(p, "--saf", help="input: saf file", type="character", default=NA)
 p <- add_argument(p, "--isPairedEnd", help="Paired-end reads, TRUE or FALSE", type="logical", default=TRUE)
-p <- add_argument(p, "--strandSpecific", help="Strand specificity (0, 1, 2)", type="numeric", default=0)
 p <- add_argument(p, "--featureType", help="Feature type in GTF annotation (default: exon)", type="character", default="exon")
 p <- add_argument(p, "--attrType", help="Attribute type in GTF annotation (default: gene_id)", type="character", default="gene_id")
 p <- add_argument(p, "--output", help="Output prefix", type="character")