ChangeLog.txt

+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>
 

debian/changelog

+last-align (1047-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 24 Jan 2020 16:21:19 +0100
+
 last-align (1045-1) unstable; urgency=medium
 
   * Team upload.

debian/patches/2to3.patch

@@ -3,8 +3,6 @@ Bug-Debian: https://bugs.debian.org/943148
 Author: Andreas Tille <tille@debian.org>
 Last-Update: Fri, 22 Nov 2019 11:23:44 +0100
 
-Index: last-align/scripts/last-dotplot
-===================================================================
 --- last-align.orig/scripts/last-dotplot
 +++ last-align/scripts/last-dotplot
 @@ -1,4 +1,4 @@
@@ -13,7 +11,7 @@ Index: last-align/scripts/last-dotplot
  
  # Read pair-wise alignments in MAF or LAST tabular format: write an
  # "Oxford grid", a.k.a. dotplot.
-@@ -262,12 +262,12 @@ def mergedRanges(ranges):
+@@ -262,12 +262,12 @@
      yield oldBeg, maxEnd
  
  def mergedRangesPerSeq(coverDict):
@@ -28,7 +26,7 @@ Index: last-align/scripts/last-dotplot
  
  def trimmed(seqRanges, coverDict, minAlignedBases, maxGapFrac, endPad, midPad):
      maxEndGapFrac, maxMidGapFrac = twoValuesFromOption(maxGapFrac, ",")
-@@ -308,7 +308,7 @@ def rangesWithStrandInfo(seqRanges, stra
+@@ -308,7 +308,7 @@
  def natural_sort_key(my_string):
      '''Return a sort key for "natural" ordering, e.g. chr9 < chr10.'''
      parts = re.split(r'(\d+)', my_string)
@@ -37,7 +35,7 @@ Index: last-align/scripts/last-dotplot
      return parts
  
  def nameKey(oneSeqRanges):
-@@ -577,7 +577,7 @@ def drawJoins(im, alignments, bpPerPix,
+@@ -577,7 +577,7 @@
  def expandedSeqDict(seqDict):
      '''Allow lookup by short sequence names, e.g. chr7 as well as hg19.chr7.'''
      newDict = seqDict.copy()
@@ -46,7 +44,7 @@ Index: last-align/scripts/last-dotplot
          if "." in name:
              base = name.split(".")[-1]
              if base in newDict:  # an ambiguous case was found:
-@@ -611,7 +611,7 @@ def readBed(fileName, rangeDict):
+@@ -611,7 +611,7 @@
          yield layer, color, seqName, beg, end
  
  def commaSeparatedInts(text):
@@ -55,8 +53,6 @@ Index: last-align/scripts/last-dotplot
  
  def readGenePred(opts, fileName, rangeDict):
      for line in myOpen(fileName):
-Index: last-align/scripts/last-map-probs
-===================================================================
 --- last-align.orig/scripts/last-map-probs
 +++ last-align/scripts/last-map-probs
 @@ -1,4 +1,4 @@
@@ -65,8 +61,6 @@ Index: last-align/scripts/last-map-probs
  
  # Copyright 2010, 2011, 2012, 2014 Martin C. Frith
  
-Index: last-align/scripts/last-postmask
-===================================================================
 --- last-align.orig/scripts/last-postmask
 +++ last-align/scripts/last-postmask
 @@ -1,4 +1,4 @@
@@ -75,7 +69,7 @@ Index: last-align/scripts/last-postmask
  
  # Copyright 2014 Martin C. Frith
  
-@@ -37,7 +37,7 @@ def complement(base):
+@@ -37,7 +37,7 @@
  
  def fastScoreMatrix(rowHeads, colHeads, matrix, deleteCost, insertCost):
      matrixLen = 128
@@ -84,17 +78,15 @@ Index: last-align/scripts/last-postmask
      fastMatrix = [[defaultScore for i in range(matrixLen)]
                    for j in range(matrixLen)]
      for i, x in enumerate(rowHeads):
-@@ -111,7 +111,7 @@ def doOneFile(lines):
+@@ -111,7 +111,7 @@
                      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 > 1 and max(list(map(len, fields))) == 1:
+-                if nf > 2 and max(map(len, fields)) == 1:
++                if nf > 2 and max(list(map(len, fields))) == 1:
                      colHeads = fields[1:]
              elif nf == len(colHeads) + 2 and len(fields[1]) == 1:
                  rowHeads.append(fields[1])
-Index: last-align/scripts/last-train
-===================================================================
 --- last-align.orig/scripts/last-train
 +++ last-align/scripts/last-train
 @@ -1,4 +1,4 @@
@@ -103,7 +95,7 @@ Index: last-align/scripts/last-train
  # Copyright 2015 Martin C. Frith
  
  # References:
-@@ -248,7 +248,7 @@ def writeScoreMatrix(outFile, matrix, pr
+@@ -248,7 +248,7 @@
      writeMatrixBody(outFile, prefix, alphabet, matrix, "%6s")
  
  def matProbsFromCounts(counts, opts):
@@ -112,8 +104,6 @@ Index: last-align/scripts/last-train
      if opts.revsym:  # add complement (reverse strand) substitutions
          counts = [[counts[i][j] + counts[-1-i][-1-j] for j in r] for i in r]
      if opts.matsym:  # symmetrize the substitution matrix
-Index: last-align/scripts/maf-convert
-===================================================================
 --- last-align.orig/scripts/maf-convert
 +++ last-align/scripts/maf-convert
 @@ -1,4 +1,4 @@
@@ -122,8 +112,6 @@ Index: last-align/scripts/maf-convert
  # Copyright 2010, 2011, 2013, 2014 Martin C. Frith
  # Read MAF-format alignments: write them in other formats.
  # Seems to work with Python 2.x, x>=6
-Index: last-align/scripts/maf-cut
-===================================================================
 --- last-align.orig/scripts/maf-cut
 +++ last-align/scripts/maf-cut
 @@ -1,4 +1,4 @@
@@ -132,7 +120,7 @@ Index: last-align/scripts/maf-cut
  
  from __future__ import print_function
  
-@@ -70,12 +70,12 @@ def cutMafRecords(mafLines, alnBeg, alnE
+@@ -70,12 +70,12 @@
  
  def mafFieldWidths(mafRecords):
      sRecords = (i for i in mafRecords if i[0] == "s")
@@ -148,8 +136,6 @@ Index: last-align/scripts/maf-cut
      print("%*s %-*s %*s %*s %*s %*s %*s" % tuple(formatParams))
  
  def cutOneMaf(cutRange, mafLines):
-Index: last-align/scripts/maf-join
-===================================================================
 --- last-align.orig/scripts/maf-join
 +++ last-align/scripts/maf-join
 @@ -1,4 +1,4 @@
@@ -158,7 +144,7 @@ Index: last-align/scripts/maf-join
  
  # Copyright 2009, 2010, 2011 Martin C. Frith
  
-@@ -229,7 +229,7 @@ def nextWindow(window, theInput, referen
+@@ -229,7 +229,7 @@
          while True:
              maf = theInput.peek()
              if maf.after(referenceMaf): break
@@ -167,8 +153,6 @@ Index: last-align/scripts/maf-join
              if not maf.before(referenceMaf): yield maf
      except StopIteration: pass
  
-Index: last-align/scripts/maf-swap
-===================================================================
 --- last-align.orig/scripts/maf-swap
 +++ last-align/scripts/maf-swap
 @@ -1,4 +1,4 @@
@@ -177,7 +161,7 @@ Index: last-align/scripts/maf-swap
  
  # Read MAF-format alignments, and write them, after moving the Nth
  # sequence to the top in each alignment.
-@@ -69,12 +69,12 @@ def flippedMafRecords(mafLines):
+@@ -69,12 +69,12 @@
  
  def sLineFieldWidths(mafLines):
      sLines = (i for i in mafLines if i[0] == "s")

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:
@@ -402,6 +403,7 @@ def scoresAndScale(originalScale, matParams, delRatios, insRatios):
         delCosts = gapCostsFromProbRatios(originalScale, *delRatios)
         insCosts = gapCostsFromProbRatios(originalScale, *insRatios)
         scale = balancedScale(originalScale, matScores, delCosts, insCosts)
+        if scale > 0:
             rowFreqs = homogeneousLetterFreqs(scale, zip(*matScores))
             colFreqs = homogeneousLetterFreqs(scale, matScores)
             if all(i >= 0 for i in rowFreqs + colFreqs):

src/version.hh

-"1045"
+"1047"