Update docstring for new demo

Author: geomesch

mixalime/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '2.12.9'
+__version__ = '2.12.10'
 import importlib
 
 __min_reqs__ = [

mixalime/create.py

@@ -218,7 +218,8 @@ def file_to_table(filename: str, counts=None, min_qual=10, min_cnt=5,
                         lt.append((name, row.ref, ','.join(row.alts)))
                     else:
                         if snp_bad_check and lt[1][-1] != bad:
-                            raise Exception(f'SNV at {chrom}:{start} comes from at least two different BADs: {bad} and {lt[1][-1]}.')
+                            raise Exception(f'SNV at {chrom}:{start} comes from at least two different BADs: {bad} and {lt[1][-1]}.'
+                                            ' If that is expected, consider setting --no-snp-bad-check flag.')
                     lt.append((filename_id, ref, alt, bad))
         if flag and snps_set is not None:
             snps_set[bad].add((chrom, start))

mixalime/main.py

@@ -239,7 +239,8 @@ def reproduce(filename: str, pretty: bool = True, check_results: bool = True):
 A [i]scorefiles[/i] folder should appear now in a working directory with plenty of BED-like files.\
 First, we'd like to parse those files into a [bold]MixALime[/bold]-friendly and efficient data structures for further usage, as well as perform some \
 basic filtering if necessary:
-[magenta]>[/magenta] [cyan]mixalime create myprojectname [i]scorefiles[/i][/cyan]
+[magenta]>[/magenta] [cyan]mixalime create myprojectname [i]scorefiles[/i] --no-snp-bad-check[/cyan]
+Here, --no-snp-bad-check is necessarily for our demo: we used cancer data from the K562 cell line, and SNVs can indeed come from different BAD regions.
 Then we fit model parameters to the data with Negative Binomial distribution:
 [magenta]>[/magenta] [cyan]mixalime fit myprojectname NB[/cyan]
 Next we obtain raw p-values: