[med-svn] [pbsuite] 01/01: Add `--header` flag to blasr invocations

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch topic/blasr5
in repository pbsuite.

commit a80f892434a3a4108f1b732d68b87244b42043a7
Author: Afif Elghraoui <afif at debian.org>
Date:   Fri Dec 23 00:53:56 2016 -0800

    Add `--header` flag to blasr invocations
    
    This seems to be needed so that output files have SAM headers.
    However, we now hit issues about requiring bam input (rather than fast{a,q}.
    See https://github.com/PacificBiosciences/blasr/issues/312
---
 debian/patches/blasr-5.patch | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/debian/patches/blasr-5.patch b/debian/patches/blasr-5.patch
index e2d5fab..dcadef0 100644
--- a/debian/patches/blasr-5.patch
+++ b/debian/patches/blasr-5.patch
@@ -145,7 +145,7 @@ Last-Update: 2016-12-11
      #map consensus to refregion
      varSam = NamedTemporaryFile(suffix=".sam")
 -    cmd = "blasr %s %s -sam -bestn 1 -affineAlign -out %s" % (conOut.name, refOut.name, varSam.name)
-+    cmd = "blasr %s %s --sam --bestn 1 --affineAlign --out %s" % (conOut.name, refOut.name, varSam.name)
++    cmd = "blasr %s %s --sam --header --bestn 1 --affineAlign --out %s" % (conOut.name, refOut.name, varSam.name)
      logging.debug(cmd)
      logging.debug(exe(cmd))
      
@@ -181,7 +181,7 @@ Last-Update: 2016-12-11
              #map consensus to refregion
              varSam = NamedTemporaryFile(suffix=".sam")
 -            blasr(conOut.name, refOut.name, format="-sam", outname=varSam.name,\
-+            blasr(conOut.name, refOut.name, format="--sam", outname=varSam.name,\
++            blasr(conOut.name, refOut.name, format="--sam --header", outname=varSam.name,\
                  consensus=False) #-- would this help?
                  #or what if I fed it through leftalign?
              #os.system("cp %s ." % (refOut.name))
@@ -201,7 +201,7 @@ Last-Update: 2016-12-11
          #map consensus to refregion
          varSam = NamedTemporaryFile(suffix=".sam")
 -        blasr(conOut.name, refOut.name, format="-sam", outname=varSam.name)
-+        blasr(conOut.name, refOut.name, format="--sam", outname=varSam.name)
++        blasr(conOut.name, refOut.name, format="--sam --header ", outname=varSam.name)
              #consensus=False) -- would this help?
              #or what if I fed it through leftalign?
          
@@ -253,14 +253,14 @@ Last-Update: 2016-12-11
 -    cmd = ("blasr %s %s %s -nproc %d -bestn 1 "
 -           "-sam -clipping subread -out %s ") \
 +    cmd = ("blasr %s %s %s --nproc %d --bestn 1 "
-+           "--sam --clipping subread --out %s ") \
++           "--sam --header --clipping subread --out %s ") \
             % (inFile, refFile, sa, nproc, outFile)
      r, o, e = exe(cmd + params)
      
 -    #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))
-+    #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 --header --bestn 1 --nCandidates 20 "
 +                 #"--out %s --clipping soft --minPctIdentity 75 "
 +                 #" --noSplitSubreads") % (fq, ref, sa, nproc, out))
      
@@ -273,7 +273,7 @@ Last-Update: 2016-12-11
      global variable reference)
      """
 -    return exe("blasr {0} {1} -sa {1}.sa -nproc 4 -out {2} -sam -bestn 1"\
-+    return exe("blasr {0} {1} --sa {1}.sa --nproc 4 --out {2} --sam --bestn 1"\
++    return exe("blasr {0} {1} --sa {1}.sa --nproc 4 --out {2} --sam --header --bestn 1"\
                 .format(reads, reference, outName))
      
  @exeLog

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbsuite.git