--- a/bwa_mem.py	Tue Mar 18 07:49:22 2014 -0400
+++ b/bwa_mem.py	Fri Mar 21 12:56:15 2014 -0400
@@ -18,25 +18,6 @@
 
 import optparse, os, shutil, subprocess, sys, tempfile
 
-def stop_err( msg ):
-    sys.stderr.write( '%s\n' % msg )
-    sys.exit()
-
-def check_is_double_encoded( fastq ):
-    # check that first read is bases, not one base followed by numbers
-    bases = [ 'A', 'C', 'G', 'T', 'a', 'c', 'g', 't', 'N' ]
-    nums = [ '0', '1', '2', '3' ]
-    for line in file( fastq, 'rb'):
-        if not line.strip() or line.startswith( '@' ):
-            continue
-        if len( [ b for b in line.strip() if b in nums ] ) > 0:
-            return False
-        elif line.strip()[0] in bases and len( [ b for b in line.strip() if b in bases ] ) == len( line.strip() ):
-            return True
-        else:
-            raise Exception, 'First line in first read does not appear to be a valid FASTQ read in either base-space or color-space'
-    raise Exception, 'There is no non-comment and non-blank line in your FASTQ file'
-
 def __main__():
     descr = "bwa_mem.py: Map (long length) reads against a reference genome with BWA-MEM."
     parser = optparse.OptionParser(description=descr)
@@ -50,20 +31,20 @@
     parser.add_option( '-s', '--fileSource', help='Whether to use a previously indexed reference sequence or one form history (indexed or history)' )
     parser.add_option( '-D', '--dbkey', help='Dbkey for reference genome' )
 
-    parser.add_option( '-k', '--minEditDistSeed', default=19, type=int, help='Minimum edit distance to the seed [19]' )
-    parser.add_option( '-w', '--bandWidth', default=100, type=int, help='Band width for banded alignment [100]' )
-    parser.add_option( '-d', '--offDiagonal', default=100, type=int, help='off-diagonal X-dropoff [100]' )
-    parser.add_option( '-r', '--internalSeeds', default=1.5, type=float, help='look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]' )
-    parser.add_option( '-c', '--seedsOccurrence', default=10000, type=int, help='skip seeds with more than INT occurrences [10000]' )
-    parser.add_option( '-S', '--mateRescue', default=False, help='skip mate rescue' )
-    parser.add_option( '-P', '--skipPairing', default=False, help='skpe pairing, mate rescue performed unless -S also in use' )
-    parser.add_option( '-A', '--seqMatch', default=1, type=int, help='score of a sequence match' )
-    parser.add_option( '-B', '--mismatch', default=4, type=int, help='penalty for a mismatch' )
-    parser.add_option( '-O', '--gapOpen', default=6, type=int, help='gap open penalty' )
-    parser.add_option( '-E', '--gapExtension', default=None, help='gap extension penalty; a gap of size k cost {-O} + {-E}*k [1]' )
-    parser.add_option( '-L', '--clipping', default=5, type=int, help='penalty for clipping [5]' )
-    parser.add_option( '-U', '--unpairedReadpair', default=17, type=int, help='penalty for an unpaired read pair [17]' )
-    parser.add_option( '-p', '--interPairEnd', default=False, help='first query file consists of interleaved paired-end sequences' )
+    parser.add_option( '-k', '--minSeedLength', type=int, help='Minimum seed length [19]' )
+    parser.add_option( '-w', '--bandWidth', type=int, help='Band width for banded alignment [100]' )
+    parser.add_option( '-d', '--offDiagonal', type=int, help='Off-diagonal X-dropoff [100]' )
+    parser.add_option( '-r', '--internalSeeds', type=float, help='Look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]' )
+    parser.add_option( '-c', '--seedsOccurrence', type=int, help='Skip seeds with more than INT occurrences [10000]' )
+    parser.add_option( '-S', '--mateRescue', action='store_true', help='Skip mate rescue' )
+    parser.add_option( '-P', '--skipPairing', action='store_true', help='Skip pairing' )
+    parser.add_option( '-A', '--seqMatch', type=int, help='Score for a sequence match [1]' )
+    parser.add_option( '-B', '--mismatch', type=int, help='Penalty for a mismatch [4]' )
+    parser.add_option( '-O', '--gapOpen', type=int, help='Gap open penalty [6]' )
+    parser.add_option( '-E', '--gapExtension', type=int, help='Gap extension penalty; a gap of length k costs {-O} + {-E}*k [1]' )
+    parser.add_option( '-L', '--clipping', help='Penalty for clipping [5]' )
+    parser.add_option( '-U', '--unpairedReadpair', type=int, help='Penalty for an unpaired read pair [17]' )
+    parser.add_option( '-p', '--interPairEnd', action='store_true', help='FASTQ file consists of interleaved paired-end sequences' )
     parser.add_option( '--rgid', help='Read group identifier' )
     parser.add_option( '--rgsm', help='Sample' )
     parser.add_option( '--rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT', 'PACBIO' ], help='Platform/technology used to produce the reads' )
@@ -76,9 +57,10 @@
     parser.add_option( '--rgks', help='The array of nucleotide bases that correspond to the key sequence of each read' )
     parser.add_option( '--rgpg', help='Programs used for processing the read group' )
     parser.add_option( '--rgpi', help='Predicted median insert size' )
-    parser.add_option( '-T', '--minScore', default=30, type=int, help='minimum score to output [30]' )
-    parser.add_option( '-M', '--mark', default=False, help='mark shorter split hits as secondary (for Picard/GATK compatibility)' )
-    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
+    parser.add_option( '-T', '--minScore', type=int, help='Minimum score to output [30]' )
+    parser.add_option( '-a', '--outputAll', action='store_true', help='Output all found alignments for single-end or unpaired paired-end reads' )
+    parser.add_option( '-M', '--mark', action='store_true', help='Mark shorter split hits as secondary (for Picard/GATK compatibility)' )
+    parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', action='store_true', help='Suppress header' )
     (options, args) = parser.parse_args()
     if len(args) > 0:
         parser.error('Wrong number of arguments')
@@ -152,7 +134,7 @@
                 shutil.rmtree( tmp_index_dir )
             if os.path.exists( tmp_dir ):
                 shutil.rmtree( tmp_dir )
-            stop_err( 'Error indexing reference sequence. ' + str( e ) )
+            raise Exception, 'Error indexing reference sequence. ' + str( e )
     else:
         ref_file_name = options.ref
     # if options.illumina13qual:
@@ -161,29 +143,45 @@
     #     illumina_quals = ""
 
     # set up aligning and generate aligning command args
-    start_cmds = '-t %s ' % options.threads
-    if options.params == 'pre_set':
-        # aligning_cmds = '-t %s %s' % ( options.threads, illumina_quals )
-        #start_cmds = '-t %s ' % options.threads
-        end_cmds = ' '
-        print start_cmds, end_cmds
-
-    else:
-        end_cmds = '-k %s -w %s -d %s -r %s -c %s -A %s -B %s -O %s -L %s -U %s -T %s ' % (options.minEditDistSeed, options.bandWidth, options.offDiagonal, options.internalSeeds, options.seedsOccurrence, options.seqMatch, options.mismatch, options.gapOpen, options.clipping, options.unpairedReadpair, options.minScore)
+    start_cmds = "bwa mem -t %s" % options.threads
+    if options.interPairEnd:
+        start_cmds += ' -p'
+    if options.params != 'pre_set':
+        if options.minSeedLength is not None:
+            start_cmds += " -k %d" % options.minSeedLength
+        if options.bandWidth is not None:
+            start_cmds += " -w %d" % options.bandWidth
+        if options.offDiagonal is not None:
+            start_cmds += " -d %d" % options.offDiagonal
+        if options.internalSeeds is not None:
+            start_cmds += " -r %s" % options.internalSeeds
+        if options.seedsOccurrence is not None:
+            start_cmds += " -c %d" % options.seedsOccurrence
         if options.mateRescue:
-            end_cmds += '-S '
-            if options.skipPairing:
-                end_cmds += '-P '
-        else:
-            if options.skipPairing:
-                print "Option Error and will not be considered, you should also choose 'skip mate rescue -S' option! "
-        if options.gapExtension != None:
-            end_cmds += '-E %s ' % options.gapExtension
-
+            start_cmds += ' -S'
+        if options.skipPairing:
+            start_cmds += ' -P'
+        if options.seqMatch is not None:
+            start_cmds += " -A %d" % options.seqMatch
+        if options.mismatch is not None:
+            start_cmds += " -B %d" % options.mismatch
+        if options.gapOpen is not None:
+            start_cmds += " -O %d" % options.gapOpen
+        if options.gapExtension is not None:
+            start_cmds += " -E %d" % options.gapExtension
+        if options.clipping:
+            start_cmds += " -L %s" % options.clipping
+        if options.unpairedReadpair is not None:
+            start_cmds += " -U %d" % options.unpairedReadpair
+        if options.minScore is not None:
+            start_cmds += " -T %d" % options.minScore
+        if options.outputAll:
+            start_cmds += ' -a'
+        if options.mark:
+            start_cmds += ' -M'
         if options.rgid:
             if not options.rglb or not options.rgpl or not options.rgsm or not options.rglb:
-                stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )
-            # readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm )
+                sys.exit( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' )
             readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm )
             if options.rgpu:
                 readGroup += '\tPU:%s' % options.rgpu
@@ -201,67 +199,58 @@
                 readGroup += '\tPG:%s' % options.rgpg
             if options.rgpi:
                 readGroup += '\tPI:%s' % options.rgpi
-            end_cmds += ' -R "%s" ' % readGroup
-
-        if options.interPairEnd:
-            end_cmds += '-p %s ' % options.interPairEnd
-        if options.mark:
-            end_cmds += '-M '
-
+            start_cmds += " -R '%s'" % readGroup
 
     if options.genAlignType == 'paired':
-        cmd = 'bwa mem %s %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, rfastq, end_cmds, options.output )
+        cmd = "%s %s %s %s > %s" % ( start_cmds, ref_file_name, fastq, rfastq, options.output )
     else:
-        cmd = 'bwa mem %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, end_cmds, options.output )
+        cmd = "%s %s %s > %s" % ( start_cmds, ref_file_name, fastq, options.output )
 
   # perform alignments
     buffsize = 1048576
     try:
         # need to nest try-except in try-finally to handle 2.4
         try:
+            tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+            tmp_stderr = open( tmp, 'wb' )
+            print "The cmd is %s" % cmd
+            proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
+            returncode = proc.wait()
+            tmp_stderr.close()
+            # get stderr, allowing for case where it's very large
+            tmp_stderr = open( tmp, 'rb' )
+            stderr = ''
             try:
-                tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
-                tmp_stderr = open( tmp, 'wb' )
-                print "The cmd is %s" % cmd
-                proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
-                returncode = proc.wait()
-                tmp_stderr.close()
-                # get stderr, allowing for case where it's very large
-                tmp_stderr = open( tmp, 'rb' )
-                stderr = ''
-                try:
-                    while True:
-                        stderr += tmp_stderr.read( buffsize )
-                        if not stderr or len( stderr ) % buffsize != 0:
-                            break
-                except OverflowError:
-                    pass
-                tmp_stderr.close()
-                if returncode != 0:
-                    raise Exception, stderr
+                while True:
+                    stderr += tmp_stderr.read( buffsize )
+                    if not stderr or len( stderr ) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+            tmp_stderr.close()
+            if returncode != 0:
+                raise Exception, stderr
+        except Exception, e:
+            raise Exception, 'Error generating alignments. ' + str( e )
+        # remove header if necessary
+        if options.suppressHeader:
+            tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
+            tmp_out_name = tmp_out.name
+            tmp_out.close()
+            try:
+                shutil.move( options.output, tmp_out_name )
             except Exception, e:
-                raise Exception, 'Error generating alignments. ' + str( e )
-            # remove header if necessary
-            if options.suppressHeader == 'true':
-                tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)
-                tmp_out_name = tmp_out.name
-                tmp_out.close()
-                try:
-                    shutil.move( options.output, tmp_out_name )
-                except Exception, e:
-                    raise Exception, 'Error moving output file before removing headers. ' + str( e )
-                fout = file( options.output, 'w' )
-                for line in file( tmp_out.name, 'r' ):
-                    if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):
-                        fout.write( line )
-                fout.close()
-            # check that there are results in the output file
-            if os.path.getsize( options.output ) > 0:
-                sys.stdout.write( 'BWA run on %s-end data' % options.genAlignType )
-            else:
-                raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.'
-        except Exception, e:
-            stop_err( 'The alignment failed.\n' + str( e ) )
+                raise Exception, 'Error moving output file before removing headers. ' + str( e )
+            fout = file( options.output, 'w' )
+            for line in file( tmp_out.name, 'r' ):
+                if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ):
+                    fout.write( line )
+            fout.close()
+        # check that there are results in the output file
+        if os.path.getsize( options.output ) > 0:
+            sys.stdout.write( 'BWA run on %s-end data' % options.genAlignType )
+        else:
+            raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.'
     finally:
         # clean up temp dir
         if os.path.exists( tmp_index_dir ):