[med-svn] [Git][med-team/last-align][master] 5 commits: New upstream version 1047
Michael R. Crusoe
gitlab at salsa.debian.org
Fri Jan 24 15:22:42 GMT 2020
Michael R. Crusoe pushed to branch master at Debian Med / last-align
Commits:
11143713 by Michael R. Crusoe at 2020-01-24T15:47:34+01:00
New upstream version 1047
- - - - -
ea6f892b by Michael R. Crusoe at 2020-01-24T15:47:34+01:00
routine-update: New upstream version
- - - - -
642da5ad by Michael R. Crusoe at 2020-01-24T15:47:36+01:00
Update upstream source from tag 'upstream/1047'
Update to upstream version '1047'
with Debian dir e227498dbd155a960a233daf2328787087325528
- - - - -
aac8c9ab by Michael R. Crusoe at 2020-01-24T15:49:10+01:00
freshen path
- - - - -
c542b525 by Michael R. Crusoe at 2020-01-24T16:21:54+01:00
1047-1
- - - - -
6 changed files:
- ChangeLog.txt
- debian/changelog
- debian/patches/2to3.patch
- 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>
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+last-align (1047-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Michael R. Crusoe <michael.crusoe at 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 at 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:
@@ -402,10 +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/compare/260cff78a7d4f117508c7794e9b59b07393f34b9...c542b5255854fd88896633f31bab14344642600f
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/compare/260cff78a7d4f117508c7794e9b59b07393f34b9...c542b5255854fd88896633f31bab14344642600f
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