fix: slicing of sequence paths

2 files changed, 15 insertions, 9 deletions

diff --git a/pangraph/graph.py b/pangraph/graph.py
index 4ae721d..24defa9 100644
--- a/pangraph/graph.py
+++ b/pangraph/graph.py
@@ -419,13 +419,13 @@ class Graph(object):
         ref = old_ref[hit['ref']['start']:hit['ref']['end']]
         qry = old_qry[hit['qry']['start']:hit['qry']['end']]
 
-        # print(ref.positions)
-        # print(qry.positions)
-        # # TODO: check for out of bounds accesses
-        # for tag, item in ref.positions.items():
-        #     blks = self.seqs[tag[0]][item-EXTEND:item+EXTEND]
-        #     print(f"Isolate: {tag[0]} blocks: {blks}")
-        # breakpoint("test positions")
+        print(ref.positions)
+        print(qry.positions)
+        for tag, item in ref.positions.items():
+            blks = self.seqs[tag[0]][item[0]-EXTEND:item[1]+EXTEND]
+            if len(blks) >= 3:
+                print(f"Isolate: {tag[0]} blocks: {','.join(b.id for b in blks)}")
+                breakpoint("test positions")
 
         if hit["orientation"] == Strand.Minus:
             qry = qry.rev_cmpl()
diff --git a/pangraph/sequence.py b/pangraph/sequence.py
index b2b5ce7..5414364 100644
--- a/pangraph/sequence.py
+++ b/pangraph/sequence.py
@@ -158,8 +158,14 @@ class Path(object):
             beg = index.start or 0
             end = index.stop or self.position[-1]
 
-            i = np.searchsorted(self.position, beg, side='right')
-            j = np.searchsorted(self.position, end, side='right') + 1
+            # TODO: circular slicing
+            beg = max(0, beg)
+            end = min(end, self.position[-1])
+            # if index.start < 0 or end > self.position[-1]:
+                # breakpoint(f"{index}:: need to implement circular slicing")
+
+            i = np.searchsorted(self.position, beg, side='right') - 1
+            j = np.searchsorted(self.position, end, side='left')
             assert i < j, "sorted"
             return [n.blk for n in self.nodes[i:j]]
         elif isinstance(index, int):