Correctly avoid annot coord adj. for BED input

BED input was not thoroughly checked to catch
cases where nc introns might be tagged for correction,
in which case the annotation correction subroutine was
activated without things being properly set up to handle the fact that
BED-input introns are missing key info (e.g., "phase"). For BED input,
the entire external correction subroutine is now bypassed.

intronIC/intronIC.py

@@ -372,7 +372,7 @@ def get_children(self, child_type=None):
     def get_introns(self, child_types, flat_annots):
         """
         Returns all introns based on >child_type<,
-        including any duplicates across children.
+        includng any duplicates across children.
 
         """
         introns = []
@@ -2444,44 +2444,54 @@ def _change_coords(line, coords, coord_tag, shift_tag, phase_shift):
     corrected_count = len(corrected_introns)
     if corrected_count == 0:
         return
-    # for intron in filter(attrgetter('corrected'), introns):
+
     for intron in corrected_introns:
-        corrected_count += 1
+        # corrected_count += 1
         if intron.duplicate:
             corrected_dupes += 1
+        if annotation_file is None:  # BED input
+            continue
         shift = intron.corrected
         five_exon = flattened[intron.upstream_exon]
         three_exon = flattened[intron.downstream_exon]
         # Build index of corrected coords by line number
         for ex, intron_side in zip([five_exon, three_exon], [5, 3]):
-            (cor_ex, coord_tag,
-            shift_tag, phase_shift) = _correct_exon(ex, shift, intron_side)
+            cor_ex, coord_tag, shift_tag, phase_shift = _correct_exon(ex, shift, intron_side)
             coords = (cor_ex.start, cor_ex.stop)
             corrected_exon_coords[ex.line_number] = (
                 coords, coord_tag, shift_tag, phase_shift)
 
-    # if corrected_count == 0:
-    #     return
+    corrected_unique = corrected_count - corrected_dupes
+
+    # if the input file was BED format, we won't be correcting any flanking feature coordinates so we 
+    # exit early
+    if annotation_file is None:
+        write_log(
+            '{} ({} unique, {} redundant) putatively misannotated U12-type introns identified in input',
+            corrected_count,
+            corrected_unique,
+            corrected_dupes
+        )
+        return
+
     # We now have an index of lines to modify in the annotation file
     modded_filename = FN_ANNOT
     modded_filepath = os.path.join(
         RUN_DIR, modded_filename)
-    with flex_open(annotation_file) as infile, \
-    open(modded_filepath, 'w') as outfile:
+    with flex_open(annotation_file) as infile, open(modded_filepath, 'w') as outfile:
         for ln, l in enumerate(infile):
             if ln not in corrected_exon_coords:
                 outfile.write(l)
                 continue
-            (new_coords, coord_tag,
-            shift_tag, phase_shift) = corrected_exon_coords[ln]
+            new_coords, coord_tag, shift_tag, phase_shift = corrected_exon_coords[ln]
             new_line = _change_coords(
                 l, new_coords, coord_tag, shift_tag, phase_shift)
             outfile.write(new_line + '\n')
     write_log(
         '{} ({} unique, {} redundant) putatively misannotated U12-type introns '
         'corrected in {}',
         corrected_count,
-        corrected_count - corrected_dupes,
+        corrected_unique,
         corrected_dupes,
         modded_filename
     )
@@ -4180,7 +4190,8 @@ def introns_from_bedfile(genome, bed):
                 start=start,
                 stop=stop,
                 strand=strand,
-                region=loc
+                region=loc,
+                phase='.'
             )
             intron_index[loc].append(intron)
             intron_count += 1
@@ -4764,7 +4775,6 @@ def filter_introns_write_files(
             longest_isoforms,
             ALLOW_OVERLAP, 
             LONGEST_ONLY)
-
         # this step seems redundant but it's not!
         intron.omit_check(
             MIN_INTRON_LENGTH,
@@ -4773,7 +4783,7 @@ def filter_introns_write_files(
             ALLOW_NONCANONICAL,
             ALLOW_OVERLAP, 
             LONGEST_ONLY)
-
+        
         if intron.noncanonical:
             # tag non-canonical introns in label even if being scored
             intron.dynamic_tag.add('[n]')
@@ -4786,6 +4796,7 @@ def filter_introns_write_files(
                 # across different annotations
             # if intron.duplicate is False:
                     # intron.sha1 = sha1(intron.seq.encode('utf-8')).digest()
+
         intron_name_index[intron.unique_num] = intron.get_name(SPCS, SIMPLE_NAME)
         if intron.duplicate is not False:
             duplicate_count += 1