[med-svn] [pbsuite] 02/02: s/-noSplitSubreads/--noSplitSubreads/
Andreas Tille
tille at debian.org
Sat Dec 24 13:14:20 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository pbsuite.
commit 96d6142b9bdbf01d32d2d5df4e6cd19ccc7907ef
Author: Andreas Tille <tille at debian.org>
Date: Sat Dec 24 14:14:01 2016 +0100
s/-noSplitSubreads/--noSplitSubreads/
---
debian/patches/fix_new_blasr_interface-sam.patch | 152 +++++++++++++++++++++--
1 file changed, 140 insertions(+), 12 deletions(-)
diff --git a/debian/patches/fix_new_blasr_interface-sam.patch b/debian/patches/fix_new_blasr_interface-sam.patch
index ff5ef11..8156e7e 100644
--- a/debian/patches/fix_new_blasr_interface-sam.patch
+++ b/debian/patches/fix_new_blasr_interface-sam.patch
@@ -9,28 +9,34 @@ Description: Adapt to change of command line syntax of blasr
Despite the fact that blasr documentation says '--sam' is deprecated
it seems to work better than only '-sam'
.
- It also turned out that '-affineAlign' needs to be '--affineAlign'.
+ It also turned out that '-affineAlign' needs to be '--affineAlign' as
+ well as '-noSplitSubreads' needs to be '--noSplitSubreads'.
Bug-Debian: https://bus.debian.org/844034
Author: Andreas Tille <tille at debian.org>
Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
--- a/pbsuite/honey/bampie.py
+++ b/pbsuite/honey/bampie.py
-@@ -11,11 +11,11 @@ from pbsuite.utils.setupLogging import s
+@@ -11,13 +11,13 @@ from pbsuite.utils.setupLogging import s
#Edit this string to set which parameters blasr will use by default
#DO NOT! Set --nproc, -bestn, --clipping, or any output (e.g. -out -m 5)
#Remove -noSpotSubreads if your inputs are bax.h5 files [i think]
-BLASRPARAMS = (" -affineAlign -noSplitSubreads -nCandidates 20 "
-+BLASRPARAMS = (" --affineAlign -noSplitSubreads -nCandidates 20 "
++BLASRPARAMS = (" --affineAlign --noSplitSubreads --nCandidates 20 "
"-minPctIdentity 75 -sdpTupleSize 6")
#Parameters used in the eichler experiments
- EEBLASRPARAMS = (" -maxAnchorsPerPosition 100 -advanceExactMatches 10 "
+-EEBLASRPARAMS = (" -maxAnchorsPerPosition 100 -advanceExactMatches 10 "
- "-affineAlign -affineOpen 100 -affineExtend 0 "
-+ "--affineAlign -affineOpen 100 -affineExtend 0 "
- "-insertion 5 -deletion 5 -extend -maxExtendDropoff 20 "
- "-noSplitSubreads -nCandidates 20 ")
+- "-insertion 5 -deletion 5 -extend -maxExtendDropoff 20 "
+- "-noSplitSubreads -nCandidates 20 ")
++EEBLASRPARAMS = (" --maxAnchorsPerPosition 100 --advanceExactMatches 10 "
++ "--affineAlign --affineOpen 100 --affineExtend 0 "
++ "--insertion 5 --deletion 5 -extend -maxExtendDropoff 20 "
++ "--noSplitSubreads --nCandidates 20 ")
#"-minPctIdentity 75 ") #didn't use this, but aybe should
-@@ -62,11 +62,11 @@ def callBlasr(inFile, refFile, params, n
+ #have
+
+@@ -62,13 +62,13 @@ def callBlasr(inFile, refFile, params, n
sa = ""
logging.info("Running Blasr")
cmd = ("blasr %s %s %s --nproc %d --bestn 1 "
@@ -42,8 +48,11 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
- #r,o,e = exe(("blasr %s %s %s --nproc %d -sam --bestn 1 -nCandidates 20 "
+ #r,o,e = exe(("blasr %s %s %s --nproc %d --sam --bestn 1 -nCandidates 20 "
#"--out %s --clipping soft -minPctIdentity 75 "
- #" -noSplitSubreads") % (fq, ref, sa, nproc, out))
+- #" -noSplitSubreads") % (fq, ref, sa, nproc, out))
++ #" --noSplitSubreads") % (fq, ref, sa, nproc, out))
+ if r != 0:
+ logging.error("blasr mapping failed!")
--- a/pbsuite/honey/HSpots.pyx
+++ b/pbsuite/honey/HSpots.pyx
@@ -510,7 +510,7 @@ def consensusCalling(spot, args):
@@ -88,11 +97,13 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
--- a/pbsuite/honey/HSpots.py
+++ b/pbsuite/honey/HSpots.py
-@@ -205,12 +205,12 @@ def blasr(query, target, format, nproc =
+@@ -204,13 +204,13 @@ def blasr(query, target, format, nproc =
+ % (query, target, format, nproc, outname)
#need to figure out how to m5-pie it...maybe
if consensus:
- r, o, e = exe(cmd + " -noSplitSubreads -minMatch 5 " + \
+- r, o, e = exe(cmd + " -noSplitSubreads -minMatch 5 " + \
- "-nCandidates 20 -sdpTupleSize 6 -insertion 1 -deletion 1 -bestn 1")
++ r, o, e = exe(cmd + " --noSplitSubreads -minMatch 5 " + \
+ "--nCandidates 20 --sdpTupleSize 6 --insertion 1 --deletion 1 --bestn 1")
else:
- r, o, e = exe(cmd + " -maxAnchorsPerPosition 100 "
@@ -102,7 +113,7 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
+ r, o, e = exe(cmd + " --maxAnchorsPerPosition 100 "
+ "--affineAlign --affineOpen 100 --affineExtend 0 "
+ "--insertion 10 --deletion 10 "
-+ "-noSplitSubreads --nCandidates 20 ")
++ "--noSplitSubreads --nCandidates 20 ")
logging.debug("blasr - %d - %s - %s" % (r, o, e))
@@ -115,3 +126,120 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
consensus=False) #-- would this help?
#or what if I fed it through leftalign?
#os.system("cp %s ." % (refOut.name))
+--- a/pbsuite/jelly/QFix.py
++++ b/pbsuite/jelly/QFix.py
+@@ -16,7 +16,7 @@ if __name__ == '__main__':
+ fout.write(">%s\n%s\n" % (i.name, i.seq))
+ fout.close()
+
+- print exe(("blasr input.fastq ref.fasta -bestn 2 -m 5 -noSplitSubreads > out.m5"))
++ print exe(("blasr input.fastq ref.fasta --bestn 2 -m 5 --noSplitSubreads > out.m5"))
+ print exe(("python /stornext/snfs5/next-gen/scratch/english/Jelly/"
+ "DevJelly/branches/consensusDev/GetSubs.py out.m5 input.fastq"))
+ print exe(("python /stornext/snfs5/next-gen/scratch/english/Jelly/"
+--- a/pbsuite/jelly/Assembly.py
++++ b/pbsuite/jelly/Assembly.py
+@@ -19,7 +19,7 @@ def blasr(query, target, fmt="5", bestn=
+ Simple overlapper
+ """
+ c = ("blasr %s %s -m %s --bestn %d --nCandidates %d --minMatch 8 --sdpTupleSize 6 --affineAlign "
+- "--nproc %d -noSplitSubreads --out %s -minPctIdentity 60 --minReadLength 5") % \
++ "--nproc %d --noSplitSubreads --out %s -minPctIdentity 60 --minReadLength 5") % \
+ (query, target, fmt, bestn, nCandidates, nproc, outname)
+ logging.debug(c)
+ r,o,e = exe(c)
+--- a/pbsuite/jelly/m4pie.py
++++ b/pbsuite/jelly/m4pie.py
+@@ -10,7 +10,7 @@ from pbsuite.utils.setupLogging import s
+ USAGE="""\
+ Extracts softclip bases from aligned reads and remaps them to the provided reference. Produces a unified bam with reads containing updated information about tail-mapping.
+
+-WARNING! -- Input.bam should be produced without -noSplitSubreads in blasr (before blasr was fixed in smrtanalysis 2.1)
++WARNING! -- Input.bam should be produced without --noSplitSubreads in blasr (before blasr was fixed in smrtanalysis 2.1)
+ """
+
+ def extractTails(aligns, reads, outFq, minLength=100):
+@@ -76,7 +76,7 @@ def mapTails(fq, ref, nproc=1, out="tail
+ else:
+ sa = ""
+ cmd = ("blasr %s %s %s --nproc %d -m 4 --bestn 1 --nCandidates 20 --out %s"
+- " -minPctIdentity 75 --sdpTupleSize 6 -noSplitSubreads") \
++ " -minPctIdentity 75 --sdpTupleSize 6 --noSplitSubreads") \
+ % (fq, ref, sa, nproc, out)
+
+ logging.debug(cmd)
+--- a/pbsuite/banana/Banana.py
++++ b/pbsuite/banana/Banana.py
+@@ -24,7 +24,7 @@ def blasr(query, target, nproc = 1, outn
+ Simple overlapper
+ """
+ r,o,e = exe(("blasr %s %s -m 5 --bestn 200 --nCandidates 200 --minMatch 12 "
+- "-affineExtend 3 --nproc %d -noSplitSubreads --out %s --maxScore -1000") % \
++ "-affineExtend 3 --nproc %d --noSplitSubreads --out %s --maxScore -1000") % \
+ (query, target, nproc, outname))
+
+ def m5ToOvlGraph(readNames, fileName):
+--- a/pbsuite/banana/OLCAssembly.py
++++ b/pbsuite/banana/OLCAssembly.py
+@@ -159,7 +159,7 @@ class OLCAssembly:
+ """
+ logging.info("Creating Overlap")
+ log = _exe(("blasr inputReads.fastq reference.fasta --nproc %d -m 4 "
+- "--out temp.rm4 -noSplitSubreads -useGuidedAlign --allowAdjacentIndels "#-minFrac 0.01
++ "--out temp.rm4 --noSplitSubreads -useGuidedAlign --allowAdjacentIndels "#-minFrac 0.01
+ "--nCandidates 20 --bestn 15 --minMatch 8 --maxLCPLength 16 ") % (self.options.nproc) )
+ logging.debug(log)
+ logging.info("Sorting the alignments")
+@@ -172,7 +172,7 @@ class OLCAssembly:
+ logging.info("Running Assembly")
+
+ logging.info("Creating afg file")
+- logging.debug(_exe("toAfg inputReads.fastq out.afg -noSplitSubreads"))
++ logging.debug(_exe("toAfg inputReads.fastq out.afg --noSplitSubreads"))
+
+ logging.info("Creating out.bank")
+ logging.debug(_exe("bank-transact -f -c -b out.bank -m out.afg"))
+--- a/pbsuite/banana/chunkyBlasr.py
++++ b/pbsuite/banana/chunkyBlasr.py
+@@ -10,7 +10,7 @@ clusterTemplate = Template("echo '${CMD}
+
+
+ #These are your default blasr parameters. Adjust at will.
+-parameters = "-maxScore -1000 -bestn 24 -maxLCPLength 16 -nCandidates 24 -noSplitSubreads"
++parameters = "--maxScore -1000 --bestn 24 --maxLCPLength 16 --nCandidates 24 --noSplitSubreads"
+
+
+ command = Template("blasr ${FAS} ${REF} ${SA} -m 4 -out ${OUT} -start ${START} -stride ${STRIDE} ${EXTRAPARAMS}")
+--- a/docs/JellyReadme.txt
++++ b/docs/JellyReadme.txt
+@@ -196,7 +196,7 @@ VI. Extras
+ However, if you would like to customize the parameters, be
+ sure to read the blasr documentation (blasr --help).
+
+- Always specify -noSplitSubreads in your blasr parameters.
++ Always specify --noSplitSubreads in your blasr parameters.
+
+ * <input> : Input contains information about where your input
+ data is located. First, there is the optional 'baseDir'
+--- a/docs/TemplateProtocol.xml
++++ b/docs/TemplateProtocol.xml
+@@ -6,7 +6,7 @@
+ <command notes="For PBS/Moab">echo '${CMD}' | msub -N "${JOBNAME}" -o ${STDOUT} -e ${STDERR} -l nodes=1:ppn=8,mem=48000mb</command>
+ <nJobs>1</nJobs>
+ </cluster>
+- <blasr>--minMatch 8 -sdpTupleSize 8 -minPctIdentity 75 --bestn 1 --nCandidates 10 --maxScore -500 --nproc 8 -noSplitSubreads</blasr>
++ <blasr>--minMatch 8 -sdpTupleSize 8 -minPctIdentity 75 --bestn 1 --nCandidates 10 --maxScore -500 --nproc 8 --noSplitSubreads</blasr>
+ <input baseDir="/FULL/PATH/TO__/PBJelly/lambdaExample/data/reads/">
+ <job>pacbioReads.fasta</job>
+ </input>
+--- a/docs/jellyExample/Protocol.xml
++++ b/docs/jellyExample/Protocol.xml
+@@ -1,7 +1,7 @@
+ <jellyProtocol>
+ <reference>/__PATH__/_TO_/jellyExample/data/reference/lambda.fasta</reference>
+ <outputDir>/__PATH__/_TO_/jellyExample/</outputDir>
+- <blasr>--minMatch 8 -minPctIdentity 70 --bestn 1 --nCandidates 20 --maxScore -500 --nproc 4 -noSplitSubreads</blasr>
++ <blasr>--minMatch 8 -minPctIdentity 70 --bestn 1 --nCandidates 20 --maxScore -500 --nproc 4 --noSplitSubreads</blasr>
+ <input baseDir="/__PATH__/_TO_/jellyExample/data/reads/">
+ <job>filtered_subreads.fastq</job>
+ </input>
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbsuite.git
More information about the debian-med-commit
mailing list