From a7baca99ccc2ce53c221f0f87b184315a83676a8 Mon Sep 17 00:00:00 2001 From: Hasindu Gamaarachchi Date: Fri, 1 Mar 2024 12:43:18 +0530 Subject: [PATCH] docs and errors --- docs/man.md | 2 +- src/sim.c | 7 ++++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/docs/man.md b/docs/man.md index 6d725ac..5d7cdbf 100755 --- a/docs/man.md +++ b/docs/man.md @@ -31,7 +31,7 @@ Advanced options are as below: - `--paf-ref`: in paf output, use the reference as the target instead of read (needs -c) - `--cdna`: generate cDNA reads (only valid with dna profiles and the reference must a transcriptome, experimental) - `--trans-count FILE`: simulate relative abundance using specified 2-column tsv with first column containing transcript name and the second containing the count (only for direct-rna and cDNA, experimental). You may generate this a test fatq dataset using minimap2, for example, `minimap2 -cx map-ont transcripts.fa reads.fastq --secondary=no -t20 -uf | cut -f 6 | sort | uniq -c | awk '{print$2"\t"$1}'`. -- `--trans-trunc=yes/no`: simulate transcript truncation (only for direct-rna and cDNA, experimental) [default: no] +- `--trans-trunc=yes/no`: simulate transcript truncation (only for direct-rna, experimental) [default: no] Developer options (which are not much tested and error handling) are as below: diff --git a/src/sim.c b/src/sim.c index ebdef5c..20e84fa 100644 --- a/src/sim.c +++ b/src/sim.c @@ -682,7 +682,7 @@ static void print_help(FILE *fp_help, opt_t opt, profile_t p, int64_t nreads) { fprintf(fp_help," --paf-ref in paf output, use the reference as the target instead of read (needs -c)\n"); fprintf(fp_help," --cdna generate cDNA reads (only valid with dna profiles and the reference must a transcriptome, experimental)\n"); fprintf(fp_help," --trans-count FILE simulate relative abundance using specified tsv with transcript name & count (only for direct-rna and cDNA, experimental)\n"); - fprintf(fp_help," --trans-trunc=yes/no simulate transcript truncattion (only for direct-rna and cDNA, experimental) [no]\n"); + fprintf(fp_help," --trans-trunc=yes/no simulate transcript truncattion (only for direct-rna, experimental) [no]\n"); fprintf(fp_help,"\ndeveloper options (not much tested yet):\n"); fprintf(fp_help," --digitisation FLOAT ADC digitisation [%.1f]\n",p.digitisation); @@ -933,6 +933,11 @@ int sim_main(int argc, char* argv[], double realtime0) { //check args check_args(opt_gvn, rna, opt, paf); + if((opt.flag & SQ_CDNA) && (opt.flag & SQ_TRANS_TRUNC)){ + ERROR("%s","Option --trans-trunc is not yet implemnted for --cdna."); + exit(EXIT_FAILURE); + } + if((opt.flag & SQ_CDNA) && (opt.flag & SQ_PREFIX)){ ERROR("%s","Option --prefix is not yet implemnted for --cdna."); exit(EXIT_FAILURE);