X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/fd7cf52127c9aa905aeae09b13dd4d1ee9f66e1c..d25db7c02aa07e9d4812a029753c2b8606cf35b1:/crunch_scripts/split-fastq.py

diff --git a/crunch_scripts/split-fastq.py b/crunch_scripts/split-fastq.py
index be37f043f3..1c7a36871d 100755
--- a/crunch_scripts/split-fastq.py
+++ b/crunch_scripts/split-fastq.py
@@ -16,8 +16,6 @@ inp = arvados.CollectionReader(arvados.getjobparam('reads'))
 
 manifest_list = []
 
-chunking = False #arvados.getjobparam('chunking')
-
 def nextline(reader, start):
     n = -1
     while True:
@@ -31,70 +29,13 @@ def nextline(reader, start):
             start += 128
     return n
 
-# Chunk a fastq into approximately 64 MiB chunks.  Requires that the input data
-# be decompressed ahead of time, such as using decompress-all.py.  Generates a
-# new manifest, but doesn't actually move any data around.  Handles paired
-# reads by ensuring that each chunk of a pair gets the same number of records.
-#
-# This works, but in practice is so slow that potential gains in alignment
-# performance are lost in the prep time, which is why it is currently disabled.
-#
-# A better algorithm would seek to a file position a bit less than the desired
-# chunk size and then scan ahead for the next record, making sure that record
-# was matched by the read pair.
-def splitfastq(p):
-    for i in xrange(0, len(p)):
-        p[i]["start"] = 0
-        p[i]["end"] = 0
-
-    count = 0
-    recordsize = [0, 0]
-
-    global piece
-    finish = False
-    while not finish:
-        for i in xrange(0, len(p)):
-            recordsize[i] = 0
-
-        # read next 4 lines
-        for i in xrange(0, len(p)):
-            for ln in xrange(0, 4):
-                r = nextline(p[i]["reader"], p[i]["end"]+recordsize[i])
-                if r == -1:
-                    finish = True
-                    break
-                recordsize[i] += (r+1)
-
-        splitnow = finish
-        for i in xrange(0, len(p)):
-            if ((p[i]["end"] - p[i]["start"]) + recordsize[i]) >= (64*1024*1024):
-                splitnow = True
-
-        if splitnow:
-            for i in xrange(0, len(p)):
-                global manifest_list
-                print >>sys.stderr, "Finish piece ./_%s/%s (%s %s)" % (piece, p[i]["reader"].name(), p[i]["start"], p[i]["end"])
-                manifest = []
-                manifest.extend(["./_" + str(piece)])
-                manifest.extend([d[arvados.LOCATOR] for d in p[i]["reader"]._stream._data_locators])
-                manifest.extend(["{}:{}:{}".format(seg[arvados.LOCATOR]+seg[arvados.OFFSET], seg[arvados.SEGMENTSIZE], p[i]["reader"].name().replace(' ', '\\040')) for seg in arvados.locators_and_ranges(p[i]["reader"].segments, p[i]["start"], p[i]["end"] - p[i]["start"])])
-                manifest_list.append(manifest)
-                p[i]["start"] = p[i]["end"]
-            piece += 1
-        else:
-            for i in xrange(0, len(p)):
-                p[i]["end"] += recordsize[i]
-            count += 1
-            if count % 10000 == 0:
-                print >>sys.stderr, "Record %s at %s" % (count, p[i]["end"])
-
 prog = re.compile(r'(.*?)(_[12])?\.fastq(\.gz)?$')
 
 # Look for fastq files
 for s in inp.all_streams():
     for f in s.all_files():
         name_pieces = prog.match(f.name())
-        if name_pieces != None:
+        if name_pieces is not None:
             if s.name() != ".":
                 # The downstream tool (run-command) only iterates over the top
                 # level of directories so if there are fastq files in
@@ -105,7 +46,7 @@ for s in inp.all_streams():
                 sys.exit(1)
 
             p = None
-            if name_pieces.group(2) != None:
+            if name_pieces.group(2) is not None:
                 if name_pieces.group(2) == "_1":
                     p = [{}, {}]
                     p[0]["reader"] = s.files()[name_pieces.group(0)]
@@ -114,15 +55,13 @@ for s in inp.all_streams():
                 p = [{}]
                 p[0]["reader"] = s.files()[name_pieces.group(0)]
 
-            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
+            if p is not None:
+                for i in xrange(0, len(p)):
+                    m = p[i]["reader"].as_manifest().split()
+                    m[0] = "./_" + str(piece)
+                    manifest_list.append(m)
+                piece += 1
 
-manifest_text = "\n".join(" ".join(m) for m in manifest_list)
+manifest_text = "\n".join(" ".join(m) for m in manifest_list) + "\n"
 
 arvados.current_task().set_output(manifest_text)