help options

hasindu2008 · Feb 19, 2024 · 267a381 · 267a381
1 parent b532c1e
commit 267a381
Show file tree

Hide file tree

Showing 2 changed files with 16 additions and 5 deletions.
diff --git a/docs/man.md b/docs/man.md
@@ -29,6 +29,9 @@ Advanced options are as below:
 -  `--prefix=yes/no`: generate prefixes such as adaptor (and polya for RNA). [default: no]
 -  `--seed INT`: seed for random generators (if 0, will be autogenerated). Giving the same seed will produce same results. [default: 0]
 - `--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)
+- `--trans-trunc=yes/no`: simulate transcript truncation (only for direct-rna and cDNA, experimental) [default: no]
 
 Developer options (which are not much tested and error handling) are as below:
 
@@ -37,5 +40,5 @@ Developer options (which are not much tested and error handling) are as below:
 -  `--range FLOAT`:              ADC range (see [here](https://hasindu2008.github.io/slow5specs/summary))
 -  `--offset-mean FLOAT`:        ADC offset mean (see [here](https://hasindu2008.github.io/slow5specs/summary))
 -  `--offset-std FLOAT`:         ADC offset standard deviation (see [here](https://hasindu2008.github.io/slow5specs/summary))
--  `--median-before-mean`:      Median before mean (see [here](https://hasindu2008.github.io/slow5specs/summary))
--  `--median-before-std`:       Median before standard deviation (see [here](https://hasindu2008.github.io/slow5specs/summary))
+-  `--median-before-mean`:       Median before mean (see [here](https://hasindu2008.github.io/slow5specs/summary))
+-  `--median-before-std`:        Median before standard deviation (see [here](https://hasindu2008.github.io/slow5specs/summary))
diff --git a/src/sim.c b/src/sim.c
@@ -680,9 +680,9 @@ static void print_help(FILE *fp_help, opt_t opt, profile_t p, int64_t nreads) {
     fprintf(fp_help,"   --prefix=yes|no            generate prefixes such as adaptor (and polya for RNA) [no]\n");
     fprintf(fp_help,"   --seed INT                 seed or random generators (if 0, will be autogenerated) [%ld]\n",opt.seed);
     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 transciptome)\n");
-    fprintf(fp_help,"   --trans-count FILE         simulate relative abundance using specified tsv with transcript name & count  (only for direct-rna and cdna)\n");
-    fprintf(fp_help,"   --trans-trunc=yes/no       simulate transcript truncatation (only for direct-rna and cdna) [no]\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,"\ndeveloper options (not much tested yet):\n");
     fprintf(fp_help,"   --digitisation FLOAT       ADC digitisation [%.1f]\n",p.digitisation);
@@ -908,12 +908,15 @@ int sim_main(int argc, char* argv[], double realtime0) {
         } else if (c == 0 && longindex == 32){ //transcript count
             trans_count = optarg;
             opt_gvn.trans_count = 1;
+            WARNING("%s","Option --trans-count is experimental. Please report any issues.")
         } else if (c == 0 && longindex == 33){ //transcript trunctate
             opt_gvn.trans_trunc = 1;
             yes_or_no(&opt, SQ_TRANS_TRUNC, longindex, optarg, 1);
+            WARNING("%s","Option --trans-trunc is experimental. Please report any issues.")
         } else if (c == 0 && longindex == 34){ //cdna
             opt_gvn.cdna = 1;
             opt.flag |= SQ_CDNA;
+            WARNING("%s","Option --cdna is experimental. Please report any issues.")
         } else if (c == '?'){
             exit(EXIT_FAILURE);
         } else {
@@ -930,6 +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_PREFIX)){
+        ERROR("%s","Option --prefix is not yet implemnted for --cdna.");
+        exit(EXIT_FAILURE);
+    }
+
     if (opt.seed == 0){
         opt.seed = realtime0;
         VERBOSE("Using random seed: %ld",opt.seed);