#!/usr/bin/env python
"""
Originally written by Kelly Vincent
pretty output and additional picard wrappers by Ross Lazarus for rgenetics
Runs all available wrapped Picard tools.
usage: picard_wrapper.py [options]
code Ross wrote licensed under the LGPL
see http://www.gnu.org/copyleft/lesser.html
"""

import optparse, os, sys, subprocess, tempfile, shutil, time, logging

galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Galaxy %s tool output - see http://getgalaxy.org/" />
<title></title>
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
</head>
<body>
<div class="document">
"""
galhtmlattr = """Galaxy tool %s run at %s</b><br/>"""
galhtmlpostfix = """</div></body></html>\n"""


def stop_err( msg ):
    sys.stderr.write( '%s\n' % msg )
    sys.exit()
    

def timenow():
    """return current time as a string
"""
    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))


class PicardBase():
    """
simple base class with some utilities for Picard
adapted and merged with Kelly Vincent's code april 2011 Ross
lots of changes...
"""
    
    def __init__(self, opts=None,arg0=None):
        """ common stuff needed at init for a picard tool
"""
        assert opts <> None, 'PicardBase needs opts at init'
        self.opts = opts
        if self.opts.outdir == None:
             self.opts.outdir = os.getcwd() # fixmate has no html file eg so use temp dir
        assert self.opts.outdir <> None,'## PicardBase needs a temp directory if no output directory passed in'
        self.picname = self.baseName(opts.jar)
        if self.picname.startswith('picard'):
            self.picname = opts.picard_cmd # special case for some tools like replaceheader?
        self.progname = self.baseName(arg0)
        self.version = '0.002'
        self.delme = [] # list of files to destroy
        self.title = opts.title
        self.inputfile = opts.input
        try:
            os.makedirs(opts.outdir)
        except:
            pass
        try:
            os.makedirs(opts.tmpdir)
        except:
            pass
        self.log_filename = os.path.join(self.opts.outdir,'%s.log' % self.picname)
        self.metricsOut = os.path.join(opts.outdir,'%s.metrics.txt' % self.picname)
        self.setLogging(logfname=self.log_filename)
 
    def baseName(self,name=None):
        return os.path.splitext(os.path.basename(name))[0]

    def setLogging(self,logfname="picard_wrapper.log"):
        """setup a logger
"""
        logging.basicConfig(level=logging.INFO,
                    filename=logfname,
                    filemode='a')


    def readLarge(self,fname=None):
        """ read a potentially huge file.
"""
        try:
            # get stderr, allowing for case where it's very large
            tmp = open( fname, 'rb' )
            s = ''
            buffsize = 1048576
            try:
                while True:
                    more = tmp.read( buffsize )
                    if len(more) > 0:
                        s += more
                    else:
                        break
            except OverflowError:
                pass
            tmp.close()
        except Exception, e:
            stop_err( 'Read Large Exception : %s' % str( e ) )
        return s
    
    def runCL(self,cl=None,output_dir=None):
        """ construct and run a command line
we have galaxy's temp path as opt.temp_dir so don't really need isolation
sometimes stdout is needed as the output - ugly hacks to deal with potentially vast artifacts
"""
        assert cl <> None, 'PicardBase runCL needs a command line as cl'
        if output_dir == None:
            output_dir = self.opts.outdir
        if type(cl) == type([]):
            cl = ' '.join(cl)
        fd,templog = tempfile.mkstemp(dir=output_dir,suffix='rgtempRun.txt')
        tlf = open(templog,'wb')
        fd,temperr = tempfile.mkstemp(dir=output_dir,suffix='rgtempErr.txt')
        tef = open(temperr,'wb')
        process = subprocess.Popen(cl, shell=True, stderr=tef, stdout=tlf, cwd=output_dir)
        rval = process.wait()
        tlf.close()
        tef.close()
        stderrs = self.readLarge(temperr)
        stdouts = self.readLarge(templog)
        if rval > 0:
            s = '## executing %s returned status %d and stderr: \n%s\n' % (cl,rval,stderrs)
            stdouts = '%s\n%s' % (stdouts,stderrs)
        else:
            s = '## executing %s returned status %d and nothing on stderr\n' % (cl,rval)
        logging.info(s)
        os.unlink(templog) # always
        os.unlink(temperr) # always
        return s, stdouts, rval # sometimes s is an output
    
    def runPic(self, jar, cl):
        """
cl should be everything after the jar file name in the command
"""
        runme = ['java -Xmx%s' % self.opts.maxjheap]
        runme.append(" -Djava.io.tmpdir='%s' " % self.opts.tmpdir)
        runme.append('-jar %s' % jar)
        runme += cl
        s,stdouts,rval = self.runCL(cl=runme, output_dir=self.opts.outdir)
        return stdouts,rval

    def samToBam(self,infile=None,outdir=None):
        """
use samtools view to convert sam to bam
"""
        fd,tempbam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.bam')
        cl = ['samtools view -h -b -S -o ',tempbam,infile]
        tlog,stdouts,rval = self.runCL(cl,outdir)
        return tlog,tempbam,rval

    def sortSam(self, infile=None,outfile=None,outdir=None):
        """
"""
        print '## sortSam got infile=%s,outfile=%s,outdir=%s' % (infile,outfile,outdir)
        cl = ['samtools sort',infile,outfile]
        tlog,stdouts,rval = self.runCL(cl,outdir)
        return tlog

    def cleanup(self):
        for fname in self.delme:
            try:
                os.unlink(fname)
            except:
                pass
                    
    def prettyPicout(self,transpose,maxrows):
        """organize picard outpouts into a report html page
"""
        res = []
        try:
            r = open(self.metricsOut,'r').readlines()
        except:
            r = []
        if len(r) > 0:
            res.append('<b>Picard on line resources</b><ul>\n')
            res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n')
            res.append('<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n')
            if transpose:
                res.append('<b>Picard output (transposed to make it easier to see)</b><hr/>\n')
            else:
                res.append('<b>Picard output</b><hr/>\n')
            res.append('<table cellpadding="3" >\n')
            dat = []
            heads = []
            lastr = len(r) - 1
            # special case for estimate library complexity hist
            thist = False
            for i,row in enumerate(r):
                if row.strip() > '':
                    srow = row.split('\t')
                    if row.startswith('#'):
                        heads.append(row.strip()) # want strings
                    else:
                        dat.append(srow) # want lists
                    if row.startswith('## HISTOGRAM'):
                        thist = True
            if len(heads) > 0:
                hres = ['<tr class="d%d"><td colspan="2">%s</td></tr>' % (i % 2,x) for i,x in enumerate(heads)]
                res += hres
                heads = []
            if len(dat) > 0:
                if transpose and not thist:
                    tdat = map(None,*dat) # transpose an arbitrary list of lists
                    tdat = ['<tr class="d%d"><td>%s</td><td>%s&nbsp;</td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat)]
                else:
                    tdat = ['\t'.join(x).strip() for x in dat] # back to strings :(
                    tdat = ['<tr class="d%d"><td colspan="2">%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(tdat)]
                res += tdat
                dat = []
            res.append('</table>\n')
        return res

    def fixPicardOutputs(self,transpose,maxloglines):
        """
picard produces long hard to read tab header files
make them available but present them transposed for readability
"""
        logging.shutdown()
        self.cleanup() # remove temp files stored in delme
        rstyle="""<style type="text/css">
tr.d0 td {background-color: oldlace; color: black;}
tr.d1 td {background-color: aliceblue; color: black;}
</style>"""
        res = [rstyle,]
        res.append(galhtmlprefix % self.progname)
        res.append(galhtmlattr % (self.picname,timenow()))
        flist = [x for x in os.listdir(self.opts.outdir) if not x.startswith('.')]
        pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']
        if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs
            for p in pdflist:
                pbase = os.path.splitext(p)[0] # removes .pdf
                imghref = '%s.jpg' % pbase
                mimghref = '%s-0.jpg' % pbase # multiple pages pdf -> multiple thumbnails without asking!
                if mimghref in flist:
                    imghref=mimghref # only one for thumbnail...it's a multi page pdf
                res.append('<table cellpadding="10"><tr><td>\n')
                res.append('<a href="%s"><img src="%s" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>\n' % (p,imghref))
                res.append('</tr></td></table>\n')
        if len(flist) > 0:
            res.append('<b>The following output files were created (click the filename to view/download a copy):</b><hr/>')
            res.append('<table>\n')
            for i,f in enumerate(flist):
                fn = os.path.split(f)[-1]
                res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fn))
            res.append('</table><p/>\n')
        pres = self.prettyPicout(transpose,maxloglines)
        if len(pres) > 0:
            res += pres
        l = open(self.log_filename,'r').readlines()
        llen = len(l)
        if llen > 0:
            res.append('<b>Picard Tool Run Log</b><hr/>\n')
            rlog = ['<pre>',]
            if llen > maxloglines:
                n = min(50,int(maxloglines/2))
                rlog += l[:n]
                rlog.append('------------ ## %d rows deleted ## --------------\n' % (llen-maxloglines))
                rlog += l[-n:]
            else:
                rlog += l
            rlog.append('</pre>')
            if llen > maxloglines:
                rlog.append('\n<b>## WARNING - %d log lines truncated - <a href="%s">%s</a> contains entire output</b>' % (llen - maxloglines,self.log_filename,self.log_filename))
            res += rlog
        else:
            res.append("### Odd, Picard left no log file %s - must have really barfed badly?\n" % self.log_filename)
        res.append('<hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n')
        res.append( 'generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool')
        res.append(galhtmlpostfix)
        outf = open(self.opts.htmlout,'w')
        outf.write(''.join(res))
        outf.write('\n')
        outf.close()

    def makePicInterval(self,inbed=None,outf=None):
        """
picard wants bait and target files to have the same header length as the incoming bam/sam
a meaningful (ie accurate) representation will fail because of this - so this hack
it would be far better to be able to supply the original bed untouched
Additional checking added Ross Lazarus Dec 2011 to deal with two 'bug' reports on the list
"""
        assert inbed <> None
        bed = open(inbed,'r').readlines()
        sbed = [x.split('\t') for x in bed] # lengths MUST be 5
        lens = [len(x) for x in sbed]
        strands = [x[3] for x in sbed if not x[3] in ['+','-']]
        maxl = max(lens)
        minl = min(lens)
        e = []
        if maxl <> minl:
            e.append("## Input error: Inconsistent field count in %s - please read the documentation on bait/target format requirements, fix and try again" % inbed)
        if maxl <> 5:
            e.append("## Input error: %d fields found in %s, 5 required - please read the warning and documentation on bait/target format requirements, fix and try again" % (maxl,inbed))
        if len(strands) > 0:
            e.append("## Input error: Fourth column in %s is not the required strand (+ or -) - please read the warning and documentation on bait/target format requirements, fix and try again" % (inbed))
        if len(e) > 0: # write to stderr and quit
            print >> sys.stderr, '\n'.join(e)
            sys.exit(1)
        thead = os.path.join(self.opts.outdir,'tempSamHead.txt')
        if self.opts.datatype == 'sam':
            cl = ['samtools view -H -S',self.opts.input,'>',thead]
        else:
            cl = ['samtools view -H',self.opts.input,'>',thead]
        self.runCL(cl=cl,output_dir=self.opts.outdir)
        head = open(thead,'r').readlines()
        s = '## got %d rows of header\n' % (len(head))
        logging.info(s)
        o = open(outf,'w')
        o.write(''.join(head))
        o.write(''.join(bed))
        o.close()
        return outf

    def cleanSam(self, insam=None, newsam=None, picardErrors=[],outformat=None):
        """
interesting problem - if paired, must remove mate pair of errors too or we have a new set of errors after cleaning - missing mate pairs!
Do the work of removing all the error sequences
pysam is cool
infile = pysam.Samfile( "-", "r" )
outfile = pysam.Samfile( "-", "w", template = infile )
for s in infile: outfile.write(s)

errors from ValidateSameFile.jar look like
WARNING: Record 32, Read name SRR006041.1202260, NM tag (nucleotide differences) is missing
ERROR: Record 33, Read name SRR006041.1042721, Empty sequence dictionary.
ERROR: Record 33, Read name SRR006041.1042721, RG ID on SAMRecord not found in header: SRR006041

"""
        assert os.path.isfile(insam), 'rgPicardValidate cleansam needs an input sam file - cannot find %s' % insam
        assert newsam <> None, 'rgPicardValidate cleansam needs an output new sam file path'
        removeNames = [x.split(',')[1].replace(' Read name ','') for x in picardErrors if len(x.split(',')) > 2]
        remDict = dict(zip(removeNames,range(len(removeNames))))
        infile = pysam.Samfile(insam,'rb')
        info = 'found %d error sequences in picardErrors, %d unique' % (len(removeNames),len(remDict))
        if len(removeNames) > 0:
            outfile = pysam.Samfile(newsam,'wb',template=infile) # template must be an open file
            i = 0
            j = 0
            for row in infile:
                dropme = remDict.get(row.qname,None) # keep if None
                if not dropme:
                    outfile.write(row)
                    j += 1
                else: # discard
                    i += 1
            info = '%s\n%s' % (info, 'Discarded %d lines writing %d to %s from %s' % (i,j,newsam,insam))
            outfile.close()
            infile.close()
        else: # we really want a nullop or a simple pointer copy
            infile.close()
            if newsam:
                shutil.copy(insam,newsam)
        logging.info(info)
                


def __main__():
    doFix = False # tools returning htmlfile don't need this
    doTranspose = True # default
    maxloglines = 100 # default
    #Parse Command Line
    op = optparse.OptionParser()
    # All tools
    op.add_option('-i', '--input', dest='input', help='Input SAM or BAM file' )
    op.add_option('-e', '--inputext', default=None)
    op.add_option('-o', '--output', default=None)
    op.add_option('-n', '--title', default="Pick a Picard Tool")
    op.add_option('-t', '--htmlout', default=None)
    op.add_option('-d', '--outdir', default=None)
    op.add_option('-x', '--maxjheap', default='3000m')
    op.add_option('-b', '--bisulphite', default='false')
    op.add_option('-s', '--sortorder', default='query')
    op.add_option('','--tmpdir', default='/tmp')
    op.add_option('-j','--jar',default='')
    op.add_option('','--picard-cmd',default=None)
    # Many tools
    op.add_option( '', '--output-format', dest='output_format', help='Output format' )
    op.add_option( '', '--bai-file', dest='bai_file', help='The path to the index file for the input bam file' )
    op.add_option( '', '--ref', dest='ref', help='Built-in reference with fasta and dict file', default=None )
    # CreateSequenceDictionary
    op.add_option( '', '--ref-file', dest='ref_file', help='Fasta to use as reference', default=None )
    op.add_option( '', '--species-name', dest='species_name', help='Species name to use in creating dict file from fasta file' )
    op.add_option( '', '--build-name', dest='build_name', help='Name of genome assembly to use in creating dict file from fasta file' )
    op.add_option( '', '--trunc-names', dest='trunc_names', help='Truncate sequence names at first whitespace from fasta file' )
    # MarkDuplicates
    op.add_option( '', '--remdups', default='true', help='Remove duplicates from output file' )
    op.add_option( '', '--optdupdist', default="100", help='Maximum pixels between two identical sequences in order to consider them optical duplicates.' )
    # CollectInsertSizeMetrics
    op.add_option('', '--taillimit', default="0")
    op.add_option('', '--histwidth', default="0")
    op.add_option('', '--minpct', default="0.01")
    op.add_option('', '--malevel', default='')
    op.add_option('', '--deviations', default="0.0")
    # CollectAlignmentSummaryMetrics
    op.add_option('', '--maxinsert', default="20")
    op.add_option('', '--adaptors', default='')
    # FixMateInformation and validate
    # CollectGcBiasMetrics
    op.add_option('', '--windowsize', default='100')
    op.add_option('', '--mingenomefrac', default='0.00001')
    # AddOrReplaceReadGroups
    op.add_option( '', '--rg-opts', dest='rg_opts', help='Specify extra (optional) arguments with full, otherwise preSet' )
    op.add_option( '', '--rg-lb', dest='rg_library', help='Read Group Library' )
    op.add_option( '', '--rg-pl', dest='rg_platform', help='Read Group platform (e.g. illumina, solid)' )
    op.add_option( '', '--rg-pu', dest='rg_plat_unit', help='Read Group platform unit (eg. run barcode) ' )
    op.add_option( '', '--rg-sm', dest='rg_sample', help='Read Group sample name' )
    op.add_option( '', '--rg-id', dest='rg_id', help='Read Group ID' )
    op.add_option( '', '--rg-cn', dest='rg_seq_center', help='Read Group sequencing center name' )
    op.add_option( '', '--rg-ds', dest='rg_desc', help='Read Group description' )
    # ReorderSam
    op.add_option( '', '--allow-inc-dict-concord', dest='allow_inc_dict_concord', help='Allow incomplete dict concordance' )
    op.add_option( '', '--allow-contig-len-discord', dest='allow_contig_len_discord', help='Allow contig length discordance' )
    # ReplaceSamHeader
    op.add_option( '', '--header-file', dest='header_file', help='sam or bam file from which header will be read' )

    op.add_option('','--assumesorted', default='true')
    op.add_option('','--readregex', default="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*")
    #estimatelibrarycomplexity
    op.add_option('','--minid', default="5")
    op.add_option('','--maxdiff', default="0.03")
    op.add_option('','--minmeanq', default="20")
    #hsmetrics
    op.add_option('','--baitbed', default=None)
    op.add_option('','--targetbed', default=None)
    #validate
    op.add_option('','--ignoreflags', action='append', type="string")
    op.add_option('','--maxerrors', default=None)
    op.add_option('','--datatype', default=None)
    op.add_option('','--bamout', default=None)
    op.add_option('','--samout', default=None)
    #downsample
    op.add_option('','--probability', default="1")
    op.add_option('','--seed', default="1")
    #meanqualitybycycle
    op.add_option('','--pfreadsonly', default='false')
    op.add_option('','--alignedreadsonly', default='false')
    #collectrnaseqmetrics
    op.add_option('','--ignoreseq', action='append', type="string")
    op.add_option('','--minlength', default=None)
    op.add_option('','--refflat', default=None)
    op.add_option('','--strandspecificity', default=None)
    op.add_option('','--ribosomalintervals', default='null')
    op.add_option('','--rrnafragmentpercentage', default=None)

    opts, args = op.parse_args()
    opts.sortme = opts.assumesorted == 'false'
    assert opts.input <> None
    # need to add
    # instance that does all the work
    pic = PicardBase(opts,sys.argv[0])

    tmp_dir = opts.outdir
    haveTempout = False # we use this where sam output is an option
    rval = 0
    stdouts = 'Not run yet'
    # set ref and dict files to use (create if necessary)
    ref_file_name = opts.ref
    if opts.ref_file <> None:
        csd = 'CreateSequenceDictionary'
        realjarpath = os.path.split(opts.jar)[0]
        jarpath = os.path.join(realjarpath,'%s.jar' % csd) # for refseq
        tmp_ref_fd, tmp_ref_name = tempfile.mkstemp( dir=opts.tmpdir , prefix = pic.picname)
        ref_file_name = '%s.fasta' % tmp_ref_name
        # build dict
        dict_file_name = '%s.dict' % tmp_ref_name
        os.symlink( opts.ref_file, ref_file_name )
        cl = ['REFERENCE=%s' % ref_file_name]
        cl.append('OUTPUT=%s' % dict_file_name)
        cl.append('URI=%s' % os.path.basename( opts.ref_file ))
        cl.append('TRUNCATE_NAMES_AT_WHITESPACE=%s' % opts.trunc_names)
        if opts.species_name:
            cl.append('SPECIES=%s' % opts.species_name)
        if opts.build_name:
            cl.append('GENOME_ASSEMBLY=%s' % opts.build_name)
        pic.delme.append(dict_file_name)
        pic.delme.append(ref_file_name)
        pic.delme.append(tmp_ref_name)
        stdouts,rval = pic.runPic(jarpath, cl)
        # run relevant command(s)

    # define temporary output
    # if output is sam, it must have that extension, otherwise bam will be produced
    # specify sam or bam file with extension
    if opts.output_format == 'sam':
        suff = '.sam'
    else:
        suff = ''
    tmp_fd, tempout = tempfile.mkstemp( dir=opts.tmpdir, suffix=suff )

    cl = ['VALIDATION_STRINGENCY=LENIENT',]

    if pic.picname == 'AddOrReplaceReadGroups':
        # sort order to match Galaxy's default
        cl.append('SORT_ORDER=coordinate')
        # input
        cl.append('INPUT=%s' % opts.input)
        # outputs
        cl.append('OUTPUT=%s' % tempout)
        # required read groups
        cl.append('RGLB="%s"' % opts.rg_library)
        cl.append('RGPL="%s"' % opts.rg_platform)
        cl.append('RGPU="%s"' % opts.rg_plat_unit)
        cl.append('RGSM="%s"' % opts.rg_sample)
        if opts.rg_id:
            cl.append('RGID="%s"' % opts.rg_id)
        # optional read groups
        if opts.rg_seq_center:
            cl.append('RGCN="%s"' % opts.rg_seq_center)
        if opts.rg_desc:
            cl.append('RGDS="%s"' % opts.rg_desc)
        stdouts,rval = pic.runPic(opts.jar, cl)
        haveTempout = True

    elif pic.picname == 'BamIndexStats':
        tmp_fd, tmp_name = tempfile.mkstemp( dir=tmp_dir )
        tmp_bam_name = '%s.bam' % tmp_name
        tmp_bai_name = '%s.bai' % tmp_bam_name
        os.symlink( opts.input, tmp_bam_name )
        os.symlink( opts.bai_file, tmp_bai_name )
        cl.append('INPUT=%s' % ( tmp_bam_name ))
        pic.delme.append(tmp_bam_name)
        pic.delme.append(tmp_bai_name)
        pic.delme.append(tmp_name)
        stdouts,rval = pic.runPic( opts.jar, cl )
        f = open(pic.metricsOut,'a')
        f.write(stdouts) # got this on stdout from runCl
        f.write('\n')
        f.close()
        doTranspose = False # but not transposed

    elif pic.picname == 'EstimateLibraryComplexity':
        cl.append('I=%s' % opts.input)
        cl.append('O=%s' % pic.metricsOut)
        if float(opts.minid) > 0:
            cl.append('MIN_IDENTICAL_BASES=%s' % opts.minid)
        if float(opts.maxdiff) > 0.0:
            cl.append('MAX_DIFF_RATE=%s' % opts.maxdiff)
        if float(opts.minmeanq) > 0:
            cl.append('MIN_MEAN_QUALITY=%s' % opts.minmeanq)
        if opts.readregex > '':
            cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
        if float(opts.optdupdist) > 0:
            cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
        stdouts,rval = pic.runPic(opts.jar, cl)

    elif pic.picname == 'CollectAlignmentSummaryMetrics':
        # Why do we do this fakefasta thing?
        # Because we need NO fai to be available or picard barfs unless it matches the input data.
        # why? Dunno Seems to work without complaining if the .bai file is AWOL....
        fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
        try:
            os.symlink(ref_file_name,fakefasta)
        except:
            s = '## unable to symlink %s to %s - different devices? Will shutil.copy'
            info = s
            shutil.copy(ref_file_name,fakefasta)
        pic.delme.append(fakefasta)
        cl.append('ASSUME_SORTED=true')
        adaptlist = opts.adaptors.split(',')
        adaptorseqs = ['ADAPTER_SEQUENCE=%s' % x for x in adaptlist]
        cl += adaptorseqs
        cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite)
        cl.append('MAX_INSERT_SIZE=%s' % opts.maxinsert)
        cl.append('OUTPUT=%s' % pic.metricsOut)
        cl.append('R=%s' % fakefasta)
        cl.append('TMP_DIR=%s' % opts.tmpdir)
        if not opts.assumesorted.lower() == 'true': # we need to sort input
            sortedfile = '%s.sorted' % os.path.basename(opts.input)
            if opts.datatype == 'sam': # need to work with a bam
                tlog,tempbam,trval = pic.samToBam(opts.input,opts.outdir)
                pic.delme.append(tempbam)
                try:
                    tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
                except:
                    print '## exception on sorting sam file %s' % opts.input
            else: # is already bam
                try:
                    tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
                except : # bug - [bam_sort_core] not being ignored - TODO fixme
                    print '## exception %s on sorting bam file %s' % (sys.exc_info()[0],opts.input)
            cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile)))
            pic.delme.append(os.path.join(opts.outdir,sortedfile))
        else:
            cl.append('INPUT=%s' % os.path.abspath(opts.input))
        stdouts,rval = pic.runPic(opts.jar, cl)
       
        
    elif pic.picname == 'CollectGcBiasMetrics':
        assert os.path.isfile(ref_file_name),'PicardGC needs a reference sequence - cannot read %s' % ref_file_name
        # sigh. Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data.
        # why? Dunno
        fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name))
        try:
            os.symlink(ref_file_name,fakefasta)
        except:
            s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy'
            info = s
            shutil.copy(ref_file_name,fakefasta)
        pic.delme.append(fakefasta)
        x = 'rgPicardGCBiasMetrics'
        pdfname = '%s.pdf' % x
        jpgname = '%s.jpg' % x
        tempout = os.path.join(opts.outdir,'rgPicardGCBiasMetrics.out')
        temppdf = os.path.join(opts.outdir,pdfname)
        cl.append('R=%s' % fakefasta)
        cl.append('WINDOW_SIZE=%s' % opts.windowsize)
        cl.append('MINIMUM_GENOME_FRACTION=%s' % opts.mingenomefrac)
        cl.append('INPUT=%s' % opts.input)
        cl.append('OUTPUT=%s' % tempout)
        cl.append('TMP_DIR=%s' % opts.tmpdir)
        cl.append('CHART_OUTPUT=%s' % temppdf)
        cl.append('SUMMARY_OUTPUT=%s' % pic.metricsOut)
        stdouts,rval = pic.runPic(opts.jar, cl)
        if os.path.isfile(temppdf):
            cl2 = ['convert','-resize x400',temppdf,os.path.join(opts.outdir,jpgname)] # make the jpg for fixPicardOutputs to find
            s,stdouts,rval = pic.runCL(cl=cl2,output_dir=opts.outdir)
        else:
            s='### runGC: Unable to find pdf %s - please check the log for the causal problem\n' % temppdf
        lf = open(pic.log_filename,'a')
        lf.write(s)
        lf.write('\n')
        lf.close()
        
    elif pic.picname == 'CollectInsertSizeMetrics':
        """ <command interpreter="python">
picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
--histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
-j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
</command>
"""
        isPDF = 'InsertSizeHist.pdf'
        pdfpath = os.path.join(opts.outdir,isPDF)
        histpdf = 'InsertSizeHist.pdf'
        cl.append('I=%s' % opts.input)
        cl.append('O=%s' % pic.metricsOut)
        cl.append('HISTOGRAM_FILE=%s' % histpdf)
        #if opts.taillimit <> '0': # this was deprecated although still mentioned in the docs at 1.56
        # cl.append('TAIL_LIMIT=%s' % opts.taillimit)
        if opts.histwidth <> '0':
            cl.append('HISTOGRAM_WIDTH=%s' % opts.histwidth)
        if float( opts.minpct) > 0.0:
            cl.append('MINIMUM_PCT=%s' % opts.minpct)
        if float(opts.deviations) > 0.0:
            cl.append('DEVIATIONS=%s' % opts.deviations)
        if opts.malevel:
            malists = opts.malevel.split(',')
            malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists]
            cl += malist
        stdouts,rval = pic.runPic(opts.jar, cl)
        if os.path.exists(pdfpath): # automake thumbnail - will be added to html
            cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath]
            pic.runCL(cl=cl2,output_dir=opts.outdir)
        else:
            s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath
            s += 'This <b>always happens if single ended data was provided</b> to this tool,\n'
            s += 'so please double check that your input data really is paired-end NGS data.<br/>\n'
            s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>'
            logging.info(s)
        if len(stdouts) > 0:
           logging.info(stdouts)
        
    elif pic.picname == 'MarkDuplicates':
        # assume sorted even if header says otherwise
        cl.append('ASSUME_SORTED=%s' % (opts.assumesorted))
        # input
        cl.append('INPUT=%s' % opts.input)
        # outputs
        cl.append('OUTPUT=%s' % opts.output)
        cl.append('METRICS_FILE=%s' % pic.metricsOut )
        # remove or mark duplicates
        cl.append('REMOVE_DUPLICATES=%s' % opts.remdups)
        # the regular expression to be used to parse reads in incoming SAM file
        cl.append('READ_NAME_REGEX="%s"' % opts.readregex)
        # maximum offset between two duplicate clusters
        cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist)
        stdouts,rval = pic.runPic(opts.jar, cl)

    elif pic.picname == 'FixMateInformation':
        cl.append('I=%s' % opts.input)
        cl.append('O=%s' % tempout)
        cl.append('SORT_ORDER=%s' % opts.sortorder)
        stdouts,rval = pic.runPic(opts.jar,cl)
        haveTempout = True
        
    elif pic.picname == 'ReorderSam':
        # input
        cl.append('INPUT=%s' % opts.input)
        # output
        cl.append('OUTPUT=%s' % tempout)
        # reference
        cl.append('REFERENCE=%s' % ref_file_name)
        # incomplete dict concordance
        if opts.allow_inc_dict_concord == 'true':
            cl.append('ALLOW_INCOMPLETE_DICT_CONCORDANCE=true')
        # contig length discordance
        if opts.allow_contig_len_discord == 'true':
            cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true')
        stdouts,rval = pic.runPic(opts.jar, cl)
        haveTempout = True

    elif pic.picname == 'ReplaceSamHeader':
        cl.append('INPUT=%s' % opts.input)
        cl.append('OUTPUT=%s' % tempout)
        cl.append('HEADER=%s' % opts.header_file)
        stdouts,rval = pic.runPic(opts.jar, cl)
        haveTempout = True

    elif pic.picname == 'CalculateHsMetrics':
        maxloglines = 100
        baitfname = os.path.join(opts.outdir,'rgPicardHsMetrics.bait')
        targetfname = os.path.join(opts.outdir,'rgPicardHsMetrics.target')
        baitf = pic.makePicInterval(opts.baitbed,baitfname)
        if opts.targetbed == opts.baitbed: # same file sometimes
            targetf = baitf
        else:
            targetf = pic.makePicInterval(opts.targetbed,targetfname)
        cl.append('BAIT_INTERVALS=%s' % baitf)
        cl.append('TARGET_INTERVALS=%s' % targetf)
        cl.append('INPUT=%s' % os.path.abspath(opts.input))
        cl.append('OUTPUT=%s' % pic.metricsOut)
        cl.append('TMP_DIR=%s' % opts.tmpdir)
        stdouts,rval = pic.runPic(opts.jar,cl)
           
    elif pic.picname == 'ValidateSamFile':
        import pysam
        doTranspose = False
        sortedfile = os.path.join(opts.outdir,'rgValidate.sorted')
        stf = open(pic.log_filename,'w')
        tlog = None
        if opts.datatype == 'sam': # need to work with a bam
            tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir)
            try:
                tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)
            except:
                print '## exception on sorting sam file %s' % opts.input
        else: # is already bam
            try:
                tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)
            except: # bug - [bam_sort_core] not being ignored - TODO fixme
                print '## exception on sorting bam file %s' % opts.input
        if tlog:
            print '##tlog=',tlog
            stf.write(tlog)
            stf.write('\n')
        sortedfile = '%s.bam' % sortedfile # samtools does that
        cl.append('O=%s' % pic.metricsOut)
        cl.append('TMP_DIR=%s' % opts.tmpdir)
        cl.append('I=%s' % sortedfile)
        opts.maxerrors = '99999999'
        cl.append('MAX_OUTPUT=%s' % opts.maxerrors)
        if opts.ignoreflags[0] <> 'None': # picard error values to ignore
            igs = ['IGNORE=%s' % x for x in opts.ignoreflags if x <> 'None']
            cl.append(' '.join(igs))
        if opts.bisulphite.lower() <> 'false':
            cl.append('IS_BISULFITE_SEQUENCED=true')
        if opts.ref <> None or opts.ref_file <> None:
            cl.append('R=%s' % ref_file_name)
        stdouts,rval = pic.runPic(opts.jar,cl)
        if opts.datatype == 'sam':
            pic.delme.append(tempbam)
        newsam = opts.output
        outformat = 'bam'
        pe = open(pic.metricsOut,'r').readlines()
        pic.cleanSam(insam=sortedfile, newsam=newsam, picardErrors=pe,outformat=outformat)
        pic.delme.append(sortedfile) # not wanted
        stf.close()
        pic.cleanup()

####liubo added CleanSam tool####
    elif pic.picname == 'CleanSam':
        # input
        cl.append('INPUT=%s' % opts.input)
        # output
        cl.append('OUTPUT=%s' % tempout)
        stdouts,rval = pic.runPic(opts.jar, cl)
        haveTempout = True

    elif pic.picname == 'SortSam':
        cl.append('I=%s' % opts.input)
        cl.append('O=%s' % tempout)
        cl.append('SORT_ORDER=%s' % opts.sortorder)
        stdouts,rval = pic.runPic(opts.jar,cl)
        haveTempout = True

    elif pic.picname == 'BuildBamIndex':
        cl.append('I=%s' % opts.input)
        cl.append('O=%s' % tempout)
        stdouts,rval = pic.runPic(opts.jar,cl)
        haveTempout = True

    elif pic.picname == 'SamFormatConverter':
        cl.append('INPUT=%s' % opts.input)
        cl.append('OUTPUT=%s' % tempout)
        pic.runPic(opts.jar, cl)
        haveTempout = True
    elif pic.picname == "DownsampleSam":
        cl.append('I=%s' % opts.input)
        mystring = opts.output
        mystringsam = mystring + ".sam"
        cl.append('O=%s' % mystringsam)
        if float(opts.probability) > 0:
            cl.append('PROBABILITY=%s' % opts.probability)
        if float(opts.seed) > 0:
            cl.append('RANDOM_SEED=%s' % opts.seed)
        stdouts,rval = pic.runPic(opts.jar, cl)
        myoutput = mystringsam.replace(".sam", "")
        os.rename(mystringsam,myoutput)

    elif pic.picname == 'MeanQualityByCycle':
        isPDF = 'MeanQualityByCycle.pdf'
        pdfpath = os.path.join(opts.outdir,isPDF)
        histpdf = isPDF
        cl.append('I=%s' % opts.input)
        cl.append('O=%s' % pic.metricsOut)
        cl.append('CHART_OUTPUT=%s' % histpdf)
        cl.append('ASSUME_SORTED=%s' % (opts.assumesorted))
        cl.append('ALIGNED_READS_ONLY=%s' % (opts.alignedreadsonly))
        cl.append('PF_READS_ONLY=%s' % (opts.pfreadsonly))
        stdouts,rval = pic.runPic(opts.jar, cl)
        if os.path.exists(pdfpath): # automake thumbnail - will be added to html
            cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath]
            pic.runCL(cl=cl2,output_dir=opts.outdir)
        else:
            s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath
            logging.info(s)
        if len(stdouts) > 0:
           logging.info(stdouts)
           
    elif pic.picname == 'CollectRnaSeqMetrics':
        isPDF = pic.picname + '.pdf'
        pdfpath = os.path.join(opts.outdir,isPDF)
        histpdf = isPDF
        cl.append('I=%s' % opts.input)
        cl.append('O=%s' % pic.metricsOut)
        cl.append('CHART_OUTPUT=%s' % histpdf)
        cl.append('ASSUME_SORTED=%s' % (opts.assumesorted))
        cl.append('MINIMUM_LENGTH=%s' % (opts.minlength))
        cl.append('REF_FLAT=%s' % (opts.refflat))
        cl.append('STRAND_SPECIFICITY=%s' % (opts.strandspecificity))
        cl.append('RIBOSOMAL_INTERVALS=%s' % (opts.ribosomalintervals))
        cl.append('RRNA_FRAGMENT_PERCENTAGE=%s' % (opts.rrnafragmentpercentage))
        if opts.ignoreseq: # picard error values to ignore
            igs = ['IGNORE_SEQUENCE=%s' % x for x in opts.ignoreseq if x <> 'None']
            cl.append(' '.join(igs))
        if opts.malevel:
            malists = opts.malevel.split(',')
            malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists]
            cl += malist
        stdouts,rval = pic.runPic(opts.jar, cl)
        if os.path.exists(pdfpath): # automake thumbnail - will be added to html
            cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath]
            pic.runCL(cl=cl2,output_dir=opts.outdir)
        else:
            s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath
            logging.info(s)
        if len(stdouts) > 0:
           logging.info(stdouts)

    else:
        print >> sys.stderr,'picard.py got an unknown tool name - %s' % pic.picname
        sys.exit(1)
    if haveTempout:
        # Some Picard tools produced a potentially intermediate bam file.
        # Either just move to final location or create sam
        if os.path.exists(tempout):
            shutil.move(tempout, os.path.abspath(opts.output))
    if opts.htmlout <> None or doFix: # return a pretty html page
        pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines)
    if rval <> 0:
        print >> sys.stderr, '## exit code=%d; stdout=%s' % (rval,stdouts)
        # signal failure
if __name__=="__main__": __main__()
