counter and control_window_length are now computed in advance of _run…

…_one_window()

shorah/b2w.py

@@ -129,7 +129,7 @@ def _build_one_full_read(full_read: list[str], full_qualities: list[int]|list[st
     return full_read, full_qualities # TODO return same data type twice
 
 
-def _run_one_window(samfile, window_start, reference_name, window_length,
+def _run_one_window(samfile, window_start, reference_name, window_length,control_window_length,
         minimum_overlap, permitted_reads_per_location, counter,
         exact_conformance_fix_0_1_basing_in_reads, indel_map, max_ins_at_pos,
         extended_window_mode, exclude_non_var_pos_threshold):
@@ -144,11 +144,16 @@ def _run_one_window(samfile, window_start, reference_name, window_length,
         window_start + window_length # arg exclusive as per pysam convention
     )
 
+    # TODO: minimum_overlap
+    # TODO: original_window_length
+    # TODO: window_length
     original_window_length = window_length
+    window_length = control_window_length
     if extended_window_mode:
-        for pos, val in max_ins_at_pos.items():
-            if window_start <= pos < window_start + original_window_length:
-                window_length += val
+        # this is now done intilaly for all windows
+        #for pos, val in max_ins_at_pos.items():
+        #    if window_start <= pos < window_start + original_window_length:
+        #        window_length += val
         minimum_overlap *= window_length/original_window_length
 
     if exclude_non_var_pos_threshold > 0:
@@ -277,7 +282,8 @@ def _run_one_window(samfile, window_start, reference_name, window_length,
     # TODO move out of this function
     convert_to_printed_fmt = lambda x: [f'>{k[0]} {k[1]}\n{"".join(k[2])}' for k in x]
 
-    return convert_to_printed_fmt(arr), arr_read_qualities_summary, arr_read_summary, counter, window_length, pos_filter
+#    return convert_to_printed_fmt(arr), arr_read_qualities_summary, arr_read_summary, counter, window_length, pos_filter
+    return convert_to_printed_fmt(arr), arr_read_qualities_summary, arr_read_summary, pos_filter
 
 
 def parallel_run_one_window(
@@ -288,6 +294,7 @@ def parallel_run_one_window(
     idx,
     window_start,
     window_length,
+    control_window_length,
     alignment_file,
     reference_name,
     win_min_ext,
@@ -315,12 +322,15 @@ def parallel_run_one_window(
 
     logging.info(f"Working on window (1-based) @ {window_start+1}")
 
+#    (arr, arr_read_qualities_summary, arr_read_summary,
+#    counter, control_window_length, pos_filter) = _run_one_window(
     (arr, arr_read_qualities_summary, arr_read_summary,
-     counter, control_window_length, pos_filter) = _run_one_window(
+     pos_filter) = _run_one_window(
         samfile,
         window_start - 1, # make 0 based
         reference_name,
         window_length,
+        control_window_length,
         math.floor(win_min_ext * window_length),
         dict(permitted_reads_per_location), # copys dict ("pass by value")
         counter,
@@ -456,6 +466,32 @@ def parallel_run_one_window(
             )
             _write_to_file([line], f"coverage_{idx}.txt")
 
+
+
+def update_tiling(tiling, extended_window_mode, max_ins_at_pos):
+    """
+    input tiling:
+
+    return: tiling = [
+            (window_start, original_window_length, control_window_length, counter)
+            for each window
+            ]
+    """
+    update_tiling = []
+
+    for idx, (window_start, window_length) in enumerate(tiling):
+        original_window_length = window_length
+        if extended_window_mode:
+            for pos, val in max_ins_at_pos.items():
+                if window_start <= pos < window_start + original_window_length:
+                    window_length += val
+            update_tiling.append((window_start,original_window_length, window_length))
+        else:
+            update_tiling.append((window_start,original_window_length, window_length))
+
+    return update_tiling
+
+
 def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
     win_min_ext: float, maximum_reads: int, minimum_reads: int,
     reference_filename: str,
@@ -508,7 +544,7 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
         threads=max_proc #1
     )
     #reffile = pysam.FastaFile(reference_filename) --> we need to read it in each child process
-    counter = 0
+    #counter = 0 #--> counter is now coputed initially for all windows
     reference_name = tiling_strategy.get_reference_name()
     tiling = tiling_strategy.get_window_tilings()
     region_end = tiling_strategy.get_region_end()
@@ -519,8 +555,15 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
         maximum_reads
     )
 
+    tiling = update_tiling(tiling, extended_window_mode, max_ins_at_pos)
+
+    # generate counter for each window
+    # counter = window_start - 1 + control_window_length, # make 0 based
+    counter_list = [0] + [window_start- 1 + control_window_length for (window_start, window_length, control_window_length) in tiling]
+
     all_processes = []
-    for idx, (window_start, window_length) in enumerate(tiling):
+    for idx, (window_start, window_length, control_window_length) in enumerate(tiling):
+        counter = counter_list[idx]
         p = Process(
             target=parallel_run_one_window,
             args=(
@@ -531,6 +574,7 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
                 idx,
                 window_start,
                 window_length,
+                control_window_length,
                 alignment_file,
                 reference_name,
                 win_min_ext,
@@ -543,12 +587,13 @@ def build_windows(alignment_file: str, tiling_strategy: TilingStrategy,
                 exclude_non_var_pos_threshold,
                 )
             )
-        p.start()
         all_processes.append(p)
 
     for p in all_processes:
-      p.join()
-    print("here after join")
+      p.run()
+
+    #for p in all_processes:
+    #  p.join()
 
     samfile.close()