From 95c7b645c94e701169d1e3e962ae263a6fdb073d Mon Sep 17 00:00:00 2001 From: shiquan Date: Thu, 17 Oct 2024 16:07:57 +0200 Subject: [PATCH] modified: src/bam_pick.c modified: src/usage.c --- src/bam_pick.c | 3 +-- src/usage.c | 1 + 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/bam_pick.c b/src/bam_pick.c index 4b4a3e0..5a4f139 100644 --- a/src/bam_pick.c +++ b/src/bam_pick.c @@ -57,8 +57,7 @@ static int parse_args(int argc, char **argv) const char **var = 0; if (strcmp(a, "-list") == 0) var = &extract_fname; else if (strcmp(a, "-o") == 0) var = &args.output_fname; - else if (strcmp(a, "-tags") == 0) var = &tag_str; - else if (strcmp(a, "-tag") == 0) error("Did you mean -tags ?"); + else if (strcmp(a, "-tags") == 0 || strcmp(a, "-tag") == 0) var = &tag_str; else if (strcmp(a, "-h") == 0 || strcmp(a, "--help") == 0) return 1; else if (strcmp(a, "-@") == 0) var = &file_th; else if (strcmp(a, "-q") == 0) var = &mapq; diff --git a/src/usage.c b/src/usage.c index 6584b5e..ce9a34b 100644 --- a/src/usage.c +++ b/src/usage.c @@ -281,6 +281,7 @@ int anno_usage() fprintf(stderr, " Also generate junction name (chr:exon1_end-exon2_start/[+-]/Gene) in JC tag.\n"); fprintf(stderr, " -flatten Split overlapped exons into nonoverlapped bins.\n"); fprintf(stderr, " -psi Annotate exclude reads tag (ER) for each exon.\n"); + fprintf(stderr, " -vague-edge [INT] Junction reads not exactly spliced at splice site and gene ends are allowed. Used to annotate third generation reads.\n"); fprintf(stderr, "\n"); //fprintf(stderr, " -as Annotate antisense RNAs. **experiment**\n"); fprintf(stderr, " -tss Annotate reads start from TSS, designed for capped library. **experiment**\n");