Contig stitcher: ensure the order of stitched contigs

Instead of appending the newly stitched part to the end,
prepend it at the start.

This way we make sure that it will be processed on
the next loop cycle.

micall/core/contig_stitcher.py

@@ -199,13 +199,14 @@ def stitch_contigs(contigs: Iterable[GenotypedContig]):
     stitched = yield from (x for x in aligned if not isinstance(x, AlignedContig))
     aligned = [x for x in aligned if isinstance(x, AlignedContig)]
 
+    # Going left-to-right through aligned contigs.
+    aligned = list(sorted(aligned, key=lambda x: x.alignment.r_st))
     while aligned:
-        # Going left-to-right through aligned parts.
-        current = min(aligned, key=lambda x: x.alignment.r_st)
-        aligned.remove(current)
+        current = aligned.pop(0)
 
         # Filter out all contigs that are contained within the current one.
         # TODO: actually filter out if covered by multiple contigs
+        # TODO: split contigs that have big gaps in them first, otherwise they will cover too much.
         aligned = [x for x in aligned if not \
                    interval_contains((current.alignment.r_st, current.alignment.r_ei),
                                      (x.alignment.r_st, x.alignment.r_ei))]
@@ -216,7 +217,7 @@ def stitch_contigs(contigs: Iterable[GenotypedContig]):
             yield current
             continue
 
-        # Get overlaping regions
+        # Replace two contigs by their stitched version, then loop with it.
         new_contig = stitch_2_contigs(current, overlapping_contig)
         aligned.remove(overlapping_contig)
-        aligned.append(new_contig)
+        aligned.insert(0, new_contig)