docs and errors

hasindu2008 · Mar 1, 2024 · a7baca9 · a7baca9
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diff --git 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
@@ -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);