[med-svn] [pbsuite] 01/02: s/-minPctIdentity/--minPctIdentity/

[Andreas Tille]

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tille pushed a commit to branch master
in repository pbsuite.

commit f6afedb2fc163e0ca7ae006acd0b7ca2062fe8bf
Author: Andreas Tille <tille at debian.org>
Date:   Sat Dec 24 14:22:14 2016 +0100

    s/-minPctIdentity/--minPctIdentity/
---
 debian/patches/fix_new_blasr_interface-sam.patch | 25 ++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/debian/patches/fix_new_blasr_interface-sam.patch b/debian/patches/fix_new_blasr_interface-sam.patch
index 8156e7e..4bccc58 100644
--- a/debian/patches/fix_new_blasr_interface-sam.patch
+++ b/debian/patches/fix_new_blasr_interface-sam.patch
@@ -10,32 +10,36 @@ Description: Adapt to change of command line syntax of blasr
  it seems to work better than only '-sam'
  .
  It also turned out that '-affineAlign' needs to be '--affineAlign' as
- well as '-noSplitSubreads' needs to be '--noSplitSubreads'.
+ well as '-noSplitSubreads' needs to be '--noSplitSubreads' and
+ '-minPctIdentity' needs to be '--minPctIdentity'
 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
-@@ -11,13 +11,13 @@ from pbsuite.utils.setupLogging import s
+@@ -11,14 +11,14 @@ 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 "
+-               "-minPctIdentity 75 -sdpTupleSize 6")
 +BLASRPARAMS = (" --affineAlign --noSplitSubreads --nCandidates 20 "
-                "-minPctIdentity 75 -sdpTupleSize 6")
++               "--minPctIdentity 75 -sdpTupleSize 6")
  #Parameters used in the eichler experiments
 -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
 +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
++               #"--minPctIdentity 75 ") #didn't use this, but aybe should
                 #have
  
+    
 @@ -62,13 +62,13 @@ def callBlasr(inFile, refFile, params, n
          sa = ""
      logging.info("Running Blasr")
@@ -46,9 +50,10 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
      r, o, e = exe(cmd + params)
      
 -    #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 "
+-                 #"--out %s --clipping soft -minPctIdentity 75 "
 -                 #" -noSplitSubreads") % (fq, ref, sa, nproc, out))
++    #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))
      
      if r != 0:
@@ -144,7 +149,7 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
      """
      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") % \
++                 "--nproc %d --noSplitSubreads --out %s --minPctIdentity 60 --minReadLength 5") % \
                   (query, target, fmt, bestn, nCandidates, nproc, outname)
      logging.debug(c)
      r,o,e = exe(c)
@@ -164,7 +169,7 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
          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") \
++           " --minPctIdentity 75 --sdpTupleSize 6 --noSplitSubreads") \
             % (fq, ref, sa, nproc, out)
      
      logging.debug(cmd)
@@ -228,7 +233,7 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
          <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>
++    <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>
@@ -239,7 +244,7 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
      <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>
++    <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>

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