set the parameters in the rna004-min profile

hasindu2008 · Apr 12, 2024 · 7318deb · 7318deb
1 parent 1a13e09
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Showing 2 changed files with 14 additions and 15 deletions.
diff --git a/docs/profile.md b/docs/profile.md
@@ -43,16 +43,16 @@ These profile sets the following advanced parameters in squigulator.
 
 | Parameter           | dna-r10-min   | dna-r10-prom   | rna004-min   | rna004-prom   |
 |---------------------|---------------|-----------------|--------------|---------------|
-| digitisation        | 8192          | 2048            | 2048         | 2048          |
+| digitisation        | 8192          | 2048            | 8192         | 2048          |
 | sample-rate         | 4000          | 4000            | 4000         | 4000          |
 | bps                 | 400           | 400             | 130          | 130           |
-| range               | 1536.598389   | 281.345551      | TBD  | 299.432068    |
-| offset-mean         | 13.380569389  | -127.5655735    | TBD5 | -259.421128  |
-| offset-std         | 16.311471649  | 19.377283387665 | TBD | 16.010841823643 |
-| median-before-mean  | 202.154074388 | 189.87607393756 | TBD | 189.87607393756 |
-| median-before-std   | 13.406139242  | 15.788097978713 | TBD | 15.788097978713 |
-| dwell-mean          | 10.0          | 10.0            | TBD         | 31.0          |
-| dwell-std           | 4.0           | 4.0             | TBD          | 4.0           |
+| range               | 1536.598389   | 281.345551      | 1437.976685  | 299.432068    |
+| offset-mean         | 13.380569389  | -127.5655735    | 12.47686423863 | -259.421128  |
+| offset-std         | 16.311471649  | 19.377283387665 | 10.442126577137 | 16.010841823643 |
+| median-before-mean  | 202.154074388 | 189.87607393756 | 205.08496731088 | 189.87607393756 |
+| median-before-std   | 13.406139242  | 15.788097978713 | 8.6671292866233 | 15.788097978713 |
+| dwell-mean          | 10.0          | 10.0            | 31.0         | 31.0          |
+| dwell-std           | 4.0           | 4.0             | 0.0          | 0.0           |
 
 ## Determining parameters for a profile
 

diff --git a/src/sim.c b/src/sim.c
@@ -140,11 +140,11 @@ profile_t minion_rna004_rna_prof = {
     .digitisation = 8192,
     .sample_rate = 4000,
     .bps = 130,
-    .range = 1536.598389,
-    .offset_mean=13.380569389019,
-    .offset_std=16.311471649012,
-    .median_before_mean=202.15407438804,
-    .median_before_std=13.406139241768,
+    .range = 1437.976685,
+    .offset_mean=12.47686423863,
+    .offset_std=10.442126577137,
+    .median_before_mean=205.08496731088,
+    .median_before_std=8.6671292866233,
     .dwell_mean=31.0, //this must be sample_rate/bps for now
     .dwell_std=0.0
 };
@@ -172,8 +172,7 @@ static inline profile_t set_profile(char *prof_name, opt_t *opt){
         opt->flag |= SQ_R10;
         return minion_r10_dna_prof;
     }else if(strcmp(prof_name, "rna004-min") == 0){
-        ERROR("%s","Parameters not determined for rna004 MinION. Please share some data!");
-        exit(EXIT_FAILURE);
+        WARNING("%s","Parameters and models for rna004-min are still crude. If you have good IVT data, please share!");
         opt->flag |= SQ_R10;
         opt->flag |= SQ_RNA;
         return minion_rna004_rna_prof;