[med-svn] [pbsuite] 02/02: s/-sdpTupleSize/--sdpTupleSize/

[Andreas Tille]

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tille pushed a commit to branch master
in repository pbsuite.

commit ef9a146b67c174e19dcddae2257c0fa41dea6484
Author: Andreas Tille <tille at debian.org>
Date:   Sat Dec 24 14:27:56 2016 +0100

    s/-sdpTupleSize/--sdpTupleSize/
---
 debian/patches/fix_new_blasr_interface-sam.patch | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/debian/patches/fix_new_blasr_interface-sam.patch b/debian/patches/fix_new_blasr_interface-sam.patch
index 4bccc58..00f466b 100644
--- a/debian/patches/fix_new_blasr_interface-sam.patch
+++ b/debian/patches/fix_new_blasr_interface-sam.patch
@@ -10,8 +10,9 @@ 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' and
- '-minPctIdentity' needs to be '--minPctIdentity'
+ well as '-noSplitSubreads' needs to be '--noSplitSubreads',
+ '-minPctIdentity' needs to be '--minPctIdentity' and '-sdpTupleSize'
+ needs to be '--sdpTupleSize'
 Bug-Debian: https://bus.debian.org/844034
 Author: Andreas Tille <tille at debian.org>
 Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
@@ -25,7 +26,7 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
 -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 "
@@ -233,7 +234,7 @@ 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>

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