Commit c37a980a authored by Martin Frith's avatar Martin Frith
Browse files

Add last-train -R option

parent b55d26ff
......@@ -22,7 +22,9 @@ alignment, and use sequence quality data in a rigorous fashion.
Usage
-----
Please see the cookbook_.
Please see the cookbook_. **Warning:** this documentation may not
apply to older versions of LAST! You can see your version with
``lastal --version``.
Install
-------
......
......@@ -714,6 +714,7 @@ def fixedLastalArgs(opts, lastalProgName):
if opts.S: x.append("-S" + opts.S)
if opts.C: x.append("-C" + opts.C)
if opts.T: x.append("-T" + opts.T)
if opts.R: x.append("-R" + opts.R)
if opts.m: x.append("-m" + opts.m)
if opts.k: x.append("-k" + opts.k)
if opts.P: x.append("-P" + opts.P)
......@@ -831,6 +832,7 @@ def doTraining(opts, args):
ss = scoresAndScaleFunc(externalScale, matParams, delRatios, insRatios)
matScores, delCosts, insCosts, scale = ss
if opts.X: print("#last -X", opts.X)
if opts.R: print("#last -R", opts.R)
if opts.Q: print("#last -Q", opts.Q)
print("#last -t{0:.6}".format(scale))
writeGapCosts(opts, delCosts, insCosts, True, None)
......@@ -914,6 +916,8 @@ if __name__ == "__main__":
"omit gapless alignments in COUNT others with > score-per-length")
og.add_option("-T", metavar="NUMBER",
help="type of alignment: 0=local, 1=overlap (default: 0)")
og.add_option("-R", metavar="DIGITS",
help="lowercase & simple-sequence options")
og.add_option("-m", metavar="COUNT", help=
"maximum initial matches per query position (default: 10)")
og.add_option("-k", metavar="STEP", help="use initial matches starting at "
......
......@@ -114,6 +114,9 @@ Alignment options
alignments with higher score-per-length. This aims to
reduce run time.
-T NUMBER Type of alignment: 0=local, 1=overlap.
-R DIGITS Lowercase & simple-sequence options. If specified, this is
written in last-train's output, so it will override
lastal's default.
-m COUNT Maximum number of initial matches per query position.
-k STEP Look for initial matches starting only at every STEP-th
position in each query.
......
......@@ -177,7 +177,7 @@ Miscellaneous options (default settings):\n\
+ stringify(globality) + ")\n\
-n: maximum gapless alignments per query position (infinity if m=0, else m)\n\
-N: stop after the first N alignments per query strand\n\
-R: repeat-marking options (the same as was used by lastdb)\n\
-R: lowercase & simple-sequence options (the same as was used by lastdb)\n\
-u: mask lowercase during extensions: 0=never, 1=gapless,\n\
2=gapless+postmask, 3=always (2 if lastdb -c and Q!=pssm, else 0)\n\
-w: suppress repeats inside exact matches, offset by <= this distance ("
......
......@@ -41,5 +41,4 @@ maf-convert tab $tmp.maf2 > $tmp.tab2
sed 's:/1::' $tmp.tab1 > $tmp.t1
sed 's:/2::' $tmp.tab2 > $tmp.t2
last-pair-probs $tmp.t1 $tmp.t2
} |
diff last-pair-test.out -
} | diff -u last-pair-test.out -
......@@ -15,5 +15,4 @@ PATH=../bin:$PATH
try maf-swap bs100.maf
try maf-swap -n1 90089.maf
try maf-swap -n3 ../examples/multiMito.maf
} 2>&1 |
diff -u $(basename $0 .sh).out -
} 2>&1 | diff -u $(basename $0 .sh).out -
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