Disable inflection point search for small datasets in flexiplex-filter

There are often times when it is desirable to have pipelines which work automatically on smaller datasets, especially
'example' or demo ones.

In these cases, inflection point searching is often not desirable due to the size of the datasets. In the cases where
it _is_ useful, it is strongly recommended that users first review the data manually and configure flexiplex-filter using
the -u and -l parameters. Hence, this commit disables the flexiplex-filter inflection point discovery automatically for
cases where there are under 50 unique counts, unless the -u and -l parameters are manually specified.

scripts/flexiplex_filter/main.py

@@ -5,6 +5,8 @@
 import logging as log
 import sys
 
+from typing import Optional
+
 
 def find_bounds(df, min_=None, max_=None):
     """
@@ -35,6 +37,11 @@ def find_bounds(df, min_=None, max_=None):
         # select the index of the row with low_cnt as the count
         max_ = int(df[df[col] == max_cnt].iloc[[0]].index[0])
 
+    # if max is 0, search the whole space
+    elif max_ == 0:
+        max_ = len(df) - 1
+        log.info(f"Setting lower bound to value {max_}, the last read")
+
     if min_ is None:
         log.debug("Setting upper bound to the count of read rank #50")
         min_ = 50
@@ -274,7 +281,7 @@ def n_derivative(df, x, y, window_size=9):
     )
 
 
-def find_inflection(df, bounds, output_count=False):
+def find_inflection(df, bounds, output_count: Optional[int]=False):
     """
     Searches for the inflection point. This effectively minimises the
     numerical derivative as the curve is always monotonically decreasing.
@@ -393,7 +400,7 @@ def parse_args():
         metavar="<r>",
         type=int,
         required=False,
-        help="highest rank to search",
+        help="highest rank to search. set to 0 to search to the end",
     )
 
     group_inf_d = parser.add_argument_group(
@@ -454,7 +461,7 @@ def cli():
         level=log.DEBUG if args.verbose else log.INFO,
     )
 
-    log.info("FLEXIPLEX-FILTER 1.01")
+    log.info("FLEXIPLEX-FILTER 1.02")
     if args.filename == sys.stdin:
         log.info("No filename given... getting reads from stdin...")
 
@@ -482,8 +489,24 @@ def cli():
 
     add_rank_index(df)
 
+    REQUIRED_UNIQUE_COUNTS = 50
+    unique_counts = len(df["count"].unique())
+
     if args.no_inflection:
         log.debug("--no-inflection was given, skipping inflection discovery")
+        df_filt = df
+    elif (( not args.max_rank ) and ( not args.min_rank ) and ( unique_counts < REQUIRED_UNIQUE_COUNTS ) and ( not args.graph )):
+        # when there are less than REQUIRED_UNIQUE_COUNTS unique counts, we will skip inflection point finding
+        # this is so that flexiplex-filter can still work for smaller 'example' datasets without requiring
+        # manual configuration.
+        #
+        # users who want to run flexiplex-filter on small datasets are highly recommended to specify the --graph argument,
+        # visualise the dataset, and then manually determine the maximum and minimum ranks for the search.
+
+        log.info(f"Number of unique counts is too small ({unique_counts}, threshold {REQUIRED_UNIQUE_COUNTS}), skipping inflection discovery by default.")
+        log.info("To force inflection discovery, manually inspect the data and then specify the -u and -l parameters.")
+        log.info("To show the graph, pass the parameters: --graph -l 1 -u 0")
+
         df_filt = df
     else:
         rank = args.use_predetermined_rank