[med-svn] [Git][med-team/last-align][upstream] New upstream version 1047

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch upstream at Debian Med / last-align


Commits:
11143713 by Michael R. Crusoe at 2020-01-24T15:47:34+01:00
New upstream version 1047
- - - - -


4 changed files:

- ChangeLog.txt
- scripts/last-postmask
- scripts/last-train
- src/version.hh


Changes:

=====================================
ChangeLog.txt
=====================================
@@ -1,9 +1,20 @@
+2020-01-20  Martin C. Frith  <Martin C. Frith>
+
+	* scripts/last-postmask, test/last-postmask-test.out, test/last-
+	postmask-test.sh:
+	last-postmask: fix crash on length-1 DB name
+	[1015a8df8312] [tip]
+
+	* scripts/last-train:
+	last-train: fix occasional crashes since v1020
+	[b6a6f4a9d738]
+
 2019-12-23  Martin C. Frith  <Martin C. Frith>
 
 	* src/Alignment.cc, src/GappedXdropAligner.hh,
 	src/GappedXdropAlignerDna.cc, src/mcf_simd.hh:
 	Make it usable without SSE/SIMD
-	[4270e27518ca] [tip]
+	[4270e27518ca]
 
 2019-12-20  Martin C. Frith  <Martin C. Frith>
 


=====================================
scripts/last-postmask
=====================================
@@ -111,7 +111,7 @@ def doOneFile(lines):
                     if i.startswith("B="): bIns = int(i[2:])
                     if i.startswith("e="): minScore = int(i[2:])
                     if i.startswith("S="): strandParam = int(i[2:])
-                if nf > 1 and max(map(len, fields)) == 1:
+                if nf > 2 and max(map(len, fields)) == 1:
                     colHeads = fields[1:]
             elif nf == len(colHeads) + 2 and len(fields[1]) == 1:
                 rowHeads.append(fields[1])


=====================================
scripts/last-train
=====================================
@@ -382,7 +382,7 @@ def balancedScale(nearScale, *args):
     if abs(value) <= 0:
         return nearScale
     oldLower = oldUpper = nearScale
-    while True:  # xxx
+    while oldUpper < 2 * nearScale:  # xxx ???
         newLower = oldLower / bump
         lowerValue = scoreImbalance(newLower, *args)
         if (lowerValue < 0) != (value < 0):
@@ -395,6 +395,7 @@ def balancedScale(nearScale, *args):
             func = scoreImbalance if value < 0 else negScoreImbalance
             return rootOfIncreasingFunction(func, oldUpper, newUpper, *args)
         oldUpper = newUpper
+    return 0.0
 
 def scoresAndScale(originalScale, matParams, delRatios, insRatios):
     while True:
@@ -402,10 +403,11 @@ def scoresAndScale(originalScale, matParams, delRatios, insRatios):
         delCosts = gapCostsFromProbRatios(originalScale, *delRatios)
         insCosts = gapCostsFromProbRatios(originalScale, *insRatios)
         scale = balancedScale(originalScale, matScores, delCosts, insCosts)
-        rowFreqs = homogeneousLetterFreqs(scale, zip(*matScores))
-        colFreqs = homogeneousLetterFreqs(scale, matScores)
-        if all(i >= 0 for i in rowFreqs + colFreqs):
-            return matScores, delCosts, insCosts, scale
+        if scale > 0:
+            rowFreqs = homogeneousLetterFreqs(scale, zip(*matScores))
+            colFreqs = homogeneousLetterFreqs(scale, matScores)
+            if all(i >= 0 for i in rowFreqs + colFreqs):
+                return matScores, delCosts, insCosts, scale
         print("# the integer-rounded scores are too inaccurate: "
               "doubling the scale")
         originalScale *= 2


=====================================
src/version.hh
=====================================
@@ -1 +1 @@
-"1045"
+"1047"



View it on GitLab: https://salsa.debian.org/med-team/last-align/commit/1114371359a004321568097e7d1c60eeb26e63c2

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View it on GitLab: https://salsa.debian.org/med-team/last-align/commit/1114371359a004321568097e7d1c60eeb26e63c2
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