fix fastq_parse for triplet

fastq_parse.py

@@ -30,10 +30,9 @@ def plot_statistics(statistics, condition: str, path: str):
             np.abs(pl.col('true size') - pl.col('read size')
                         ).alias('abs(true - observed)')
         )
-    print(df.filter(np.abs(pl.col('true - observed')) > 50).get_column('name').to_list())
     df = df.with_columns(pl.col('true size').mean().alias('mean size'))
     plot = (
-        ggplot(df.sample(fraction=0.1), aes(x='true size', y='true - observed', color='factor(read)')) +
+        ggplot(df.sample(fraction=1), aes(x='true size', y='true - observed', color='factor(read)')) +
         geom_point(alpha = 0.5, size = 0.1) +
         facet_wrap('~mapping')
 
@@ -93,9 +92,9 @@ def parse_read_name(read):
     """
     data = list(chain(*list(map(lambda x: re.split("[:|-]", x), read[0].split("_")))))
     # ['@chr1', '5', '1005', 'chr1', '113485', '114485', '83', '2', '[0,0]', 'chr1', '5', '1005', 'chr1', '113485', '114485', '83', '2', 'S']
-    if len(data) < 9:
-        length = int(data[-2])
-        index = int(data[-1])
+    if len(data) < 10:
+        length = int(data[-3])
+        index = int(data[-2])
         mapping = "Not split"
         combinaison = None
     else:
@@ -122,23 +121,17 @@ def eval_reads(reads: list, read_size: int):
     index, length, combinaison, mapping = parse_read_name(reads[0])
     obs_size = len(reads[index - 1][1])
     if combinaison is None:
-            return [length, obs_size, False, index, mapping, reads[0][0]]
-    # if index == 1 and mapping == 'M':
-    #     obs_size = read_size - obs_size
-    # if index == 2 and mapping == 'S':
-    #     obs_size = read_size - obs_size
+        return [length, obs_size, False, index, mapping, reads[0][0]]
     if combinaison == [0, 1]:
         return [length, obs_size, True, index, mapping, reads[0][0]]
-    elif combinaison == [0, 2]:
-        if index == 2:
-            length = read_size - length
+    if combinaison == [2, 3] and index == 1:
         return [length, obs_size, True, index, mapping, reads[0][0]]
-    elif combinaison == [1, 2]:
-        length = read_size - length
+    if combinaison == [0, 3] and index == 2:
         return [length, obs_size, True, index, mapping, reads[0][0]]
     return None
 
 
+
 if __name__ == "__main__":
     import doctest
     doctest.testmod()