Commit 11143713 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 1047

parent 73307486

ChangeLog.txt

+12 −1
Original line number Diff line number Diff line 
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

+1 −1
Original line number Diff line number Diff line
@@ -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

+7 −5
Original line number Diff line number Diff line
@@ -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

+1 −1
Original line number Diff line number Diff line 
"1045"
 
"1047"