increase min realign len default to 1kbp

schneebergerlab · Sep 9, 2024 · 44db699 · 44db699
1 parent a5759c7
commit 44db699
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/msyd/pyxfiles/realignment.pyx b/msyd/pyxfiles/realignment.pyx
@@ -31,7 +31,7 @@ import msyd.intersection as intersection
 import msyd.io as io
 
 
-cdef int _MIN_REALIGN_LEN = 200 # min length to realign regions
+cdef int _MIN_REALIGN_LEN = 1000 # min length to realign regions
 cdef int _MIN_SYN_ID = 80 # minimum % identity for a region to be considered syntenic
 cdef int _MAX_REALIGN = 0 # max number of haplotypes to realign to; set to 0 to realign without limit
 cdef int _NULL_CNT = 100 # number of separators to use between blocks during alignment