fix: made window offset a global parameter in anticipation of a cli parameter

2 files changed, 7 insertions, 3 deletions

diff --git a/pangraph/graph.py b/pangraph/graph.py
index 1664d03..a38a4e3 100644
--- a/pangraph/graph.py
+++ b/pangraph/graph.py
@@ -21,6 +21,7 @@ from .utils    import Strand, as_string, parse_paf, panic, as_record, new_strand
 # ------------------------------------------------------------------------
 # globals
 
+WINDOW = 1000
 EXTEND = 2500
 pp = pprint.PrettyPrinter(indent=4)
 
@@ -495,12 +496,14 @@ class Graph(object):
         delta = len(blk_list)-len(shared_blks)
         if delta > 0 and num_seqs > 1:
             print(f"LEN: {delta}", end="\t")
-            for i, (left, right) in enumerate([(beg[0]-EXTEND,beg[0]), (end[1],end[1]+EXTEND)]):
+            for n, (left, right) in enumerate([(beg[0]-EXTEND,beg[0]+WINDOW), (end[1]-WINDOW,end[1]+EXTEND)]):
                 fd, path = tempfile.mkstemp()
                 try:
                     with os.fdopen(fd, 'w') as tmp:
                         for i, tag in enumerate(chain(ref.muts.keys(), qry.muts.keys())):
                             tmp.write(f">isolate_{i:04d}\n")
+                            if left == right:
+                                breakpoint("no difference")
                             blks = self.seqs[tag[0]][left:right]
                             for b in blks:
                                 tmp.write(b.extract(*tag))
@@ -513,7 +516,7 @@ class Graph(object):
                                     shell=True)
                         out, err = proc.communicate()
                         tree = Phylo.read(io.StringIO(out.decode('utf-8')), format='newick')
-                        print(f"-> NUM {i}: {tree.total_branch_length()}")
+                        print(f"-> NUM {n}: {tree.total_branch_length()}")
                 finally:
                     os.remove(path)
         else:
diff --git a/pangraph/sequence.py b/pangraph/sequence.py
index 6b9baba..c437602 100644
--- a/pangraph/sequence.py
+++ b/pangraph/sequence.py
@@ -173,7 +173,8 @@ class Path(object):
 
             i = np.searchsorted(self.position, beg, side='right') - 1
             j = np.searchsorted(self.position, end, side='left')
-            assert i < j, f"not sorted, {beg}-{end}"
+            if i > j:
+                breakpoint(f"not sorted, {beg}-{end}")
             return l + [n.blk for n in self.nodes[i:j]] + r
         elif isinstance(index, int):
             i = np.searchsorted(self.position, index, side='right') - 1