Merge pull request #447 from nextstrain/fix-andv

andes: adjust alignment parms, mask gappy regions for tree

Author: rneher

data/nextstrain/orthohantavirus/andv/l/pathogen.json

@@ -20,8 +20,8 @@
   "alignmentParams": {
     "penaltyGapExtend": 1,
     "penaltyGapOpen": 8,
-    "penaltyGapOpenInFrame": 9,
-    "penaltyGapOpenOutOfFrame": 10,
+    "penaltyGapOpenInFrame": 15,
+    "penaltyGapOpenOutOfFrame": 18,
     "penaltyMismatch": 1,
     "scoreMatch": 5,
     "retryReverseComplement": true,

data/nextstrain/orthohantavirus/andv/l/tree.json

@@ -20,8 +20,8 @@
   "alignmentParams": {
     "penaltyGapExtend": 1,
     "penaltyGapOpen": 8,
-    "penaltyGapOpenInFrame": 9,
-    "penaltyGapOpenOutOfFrame": 10,
+    "penaltyGapOpenInFrame": 15,
+    "penaltyGapOpenOutOfFrame": 18,
     "penaltyMismatch": 1,
     "scoreMatch": 5,
     "retryReverseComplement": true,

data/nextstrain/orthohantavirus/andv/m/pathogen.json

@@ -20,11 +20,13 @@
   "alignmentParams": {
     "penaltyGapExtend": 1,
     "penaltyGapOpen": 8,
-    "penaltyGapOpenInFrame": 9,
-    "penaltyGapOpenOutOfFrame": 10,
+    "penaltyGapOpenInFrame": 15,
+    "penaltyGapOpenOutOfFrame": 18,
     "penaltyMismatch": 1,
     "scoreMatch": 5,
     "retryReverseComplement": true,
+    "excessBandwidth": 50,
+    "terminalBandwidth": 100,
     "allowedMismatches": 10,
     "minSeedCover": 0.12,
     "minLength": 100

data/nextstrain/orthohantavirus/andv/m/tree.json

@@ -20,8 +20,8 @@
   "alignmentParams": {
     "penaltyGapExtend": 1,
     "penaltyGapOpen": 8,
-    "penaltyGapOpenInFrame": 9,
-    "penaltyGapOpenOutOfFrame": 10,
+    "penaltyGapOpenInFrame": 15,
+    "penaltyGapOpenOutOfFrame": 18,
     "penaltyMismatch": 1,
     "scoreMatch": 5,
     "retryReverseComplement": true,