[ARVADOS] updated: fd7cf52127c9aa905aeae09b13dd4d1ee9f66e1c

[git at public.curoverse.com]

Summary of changes:
 crunch_scripts/split-fastq.py | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

       via  fd7cf52127c9aa905aeae09b13dd4d1ee9f66e1c (commit)
       via  efd131427759f5a2663dea04a402054e361b7c90 (commit)
      from  b5393c72ddd855564cae2f2d798a3e4496a8d2ec (commit)

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commit fd7cf52127c9aa905aeae09b13dd4d1ee9f66e1c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Fri Aug 8 16:56:29 2014 -0400

    3373: split-fastq: Fix loop

diff --git a/crunch_scripts/split-fastq.py b/crunch_scripts/split-fastq.py
index 8b80adf..be37f04 100755
--- a/crunch_scripts/split-fastq.py
+++ b/crunch_scripts/split-fastq.py
@@ -104,6 +104,7 @@ for s in inp.all_streams():
                 print >>sys.stderr, "fastq must be at the root of the collection"
                 sys.exit(1)
 
+            p = None
             if name_pieces.group(2) != None:
                 if name_pieces.group(2) == "_1":
                     p = [{}, {}]
@@ -113,13 +114,14 @@ for s in inp.all_streams():
                 p = [{}]
                 p[0]["reader"] = s.files()[name_pieces.group(0)]
 
-            if chunking:
-                splitfastq(p)
-            else:
-                for i in xrange(0, len(p)):
-                    m = p[i]["reader"].as_manifest()[1:]
-                    manifest_list.append(["./_" + str(piece), m[:-1]])
-                piece += 1
+            if p != None:
+                if chunking:
+                    splitfastq(p)
+                else:
+                    for i in xrange(0, len(p)):
+                        m = p[i]["reader"].as_manifest()[1:]
+                        manifest_list.append(["./_" + str(piece), m[:-1]])
+                    piece += 1
 
 manifest_text = "\n".join(" ".join(m) for m in manifest_list)
 

commit efd131427759f5a2663dea04a402054e361b7c90
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Fri Aug 8 16:45:45 2014 -0400

    3373: split-fastq: Fix regex again

diff --git a/crunch_scripts/split-fastq.py b/crunch_scripts/split-fastq.py
index e242102..8b80adf 100755
--- a/crunch_scripts/split-fastq.py
+++ b/crunch_scripts/split-fastq.py
@@ -88,7 +88,7 @@ def splitfastq(p):
             if count % 10000 == 0:
                 print >>sys.stderr, "Record %s at %s" % (count, p[i]["end"])
 
-prog = re.compile(r'(.*?)(_12)?\.fastq(\.gz)?$')
+prog = re.compile(r'(.*?)(_[12])?\.fastq(\.gz)?$')
 
 # Look for fastq files
 for s in inp.all_streams():

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