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          _________________  __ __  __| _/|__|/  |_ 
         / ___\_` __ \__  \ |  |  \/ __ | | \\_  __\
        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
        \___  /|__|  (____  /____/\____ | |__||__|  
       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
pbsuite-15.8.24+dfsg/CHANGELOG.txt-11-
pbsuite-15.8.24+dfsg/CHANGELOG.txt:12:	Added downsampling to Honey.py asm instead of failing when too many
pbsuite-15.8.24+dfsg/CHANGELOG.txt-13-	reads were present. - and only for Illumina reads
##############################################
pbsuite-15.8.24+dfsg/CHANGELOG.txt-113-
pbsuite-15.8.24+dfsg/CHANGELOG.txt:114:	Honey asm downsampling needs to correctly choose 'best' reads instead of
pbsuite-15.8.24+dfsg/CHANGELOG.txt-115-	random sample
pbsuite-15.8.24+dfsg/CHANGELOG.txt-116-
pbsuite-15.8.24+dfsg/CHANGELOG.txt:117:    	Honey asm fetch 
pbsuite-15.8.24+dfsg/CHANGELOG.txt-118-        I need to fix the fetching logic for all but phrap - can i not pull
##############################################
pbsuite-15.8.24+dfsg/bin/Honey.py-22-     force      Given a BedFile of predicted variants, force search for matching
pbsuite-15.8.24+dfsg/bin/Honey.py:23:     asm        Assemble reads around a variant and remap contigs to a reference
pbsuite-15.8.24+dfsg/bin/Honey.py-24-     cpxres     Complex multi-break-point resolution (beta)
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/Honey.py-22-     force      Given a BedFile of predicted variants, force search for matching
pbsuite-15.8.24+dfsg/pbsuite/honey/Honey.py:23:     asm        Assemble reads around a variant and remap contigs to a reference
pbsuite-15.8.24+dfsg/pbsuite/honey/Honey.py-24-     cpxres     Complex multi-break-point resolution (beta)
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/bakH.py-949-        #run phrap
pbsuite-15.8.24+dfsg/pbsuite/honey/bakH.py:950:        #if asm -- consensus only 
pbsuite-15.8.24+dfsg/pbsuite/honey/bakH.py-951-        r, o, e = exe("phrap %s -minmatch 6 -minscore 20" % (foutreads.name), timeout=3)
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/bakH.py-961-        if len(results) == 0:
pbsuite-15.8.24+dfsg/pbsuite/honey/bakH.py:962:            logging.warning('no asm made ' + self.name)
pbsuite-15.8.24+dfsg/pbsuite/honey/bakH.py-963-            return [] #here is where I'd like to add just the no-consensus spot
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/bakH.py-970-        blasr(foutreads.name, foutreads.name + ".contigs", format="-m 5", nproc=1, outname=alignOut.name)
pbsuite-15.8.24+dfsg/pbsuite/honey/bakH.py:971:        # elif no asm and consensus only (faster)
pbsuite-15.8.24+dfsg/pbsuite/honey/bakH.py-972-        
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-217-        #Fetch,
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py:218:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-219-        reads = {}
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-257-        self.result = self.__assemble(reads)
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py:258:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-259-        return self.result
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-331-        #Fetch,
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py:332:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-333-        reads = []
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-352-        self.result = self.__assemble(reads)
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py:353:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-354-        return self.result
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-481-        #Fetch,
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py:482:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-483-        reads = []
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-506-        self.result = self.__assemble()
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py:507:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-508-        return self.result
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-588-        #Fetch,
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py:589:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-590-        reads = []
##############################################
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-617-        
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py:618:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/pbsuite/honey/massivePhrap.py-619-        return self.result
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/Honey.py-22-     force      Given a BedFile of predicted variants, force search for matching
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/Honey.py:23:     asm        Assemble reads around a variant and remap contigs to a reference
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/Honey.py-24-     cpxres     Complex multi-break-point resolution (beta)
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/bakH.py-949-        #run phrap
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/bakH.py:950:        #if asm -- consensus only 
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/bakH.py-951-        r, o, e = exe("phrap %s -minmatch 6 -minscore 20" % (foutreads.name), timeout=3)
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/bakH.py-961-        if len(results) == 0:
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/bakH.py:962:            logging.warning('no asm made ' + self.name)
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/bakH.py-963-            return [] #here is where I'd like to add just the no-consensus spot
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/bakH.py-970-        blasr(foutreads.name, foutreads.name + ".contigs", format="-m 5", nproc=1, outname=alignOut.name)
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/bakH.py:971:        # elif no asm and consensus only (faster)
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/bakH.py-972-        
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-217-        #Fetch,
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py:218:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-219-        reads = {}
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-257-        self.result = self.__assemble(reads)
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py:258:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-259-        return self.result
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-331-        #Fetch,
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py:332:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-333-        reads = []
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-352-        self.result = self.__assemble(reads)
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py:353:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-354-        return self.result
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-481-        #Fetch,
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py:482:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-483-        reads = []
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-506-        self.result = self.__assemble()
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py:507:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-508-        return self.result
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-588-        #Fetch,
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py:589:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-590-        reads = []
##############################################
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-617-        
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py:618:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/fix-shebang-lines.patch/pbsuite/honey/massivePhrap.py-619-        return self.result
##############################################
pbsuite-15.8.24+dfsg/.pc/blasr-5.patch/pbsuite/honey/bakH.py-949-        #run phrap
pbsuite-15.8.24+dfsg/.pc/blasr-5.patch/pbsuite/honey/bakH.py:950:        #if asm -- consensus only 
pbsuite-15.8.24+dfsg/.pc/blasr-5.patch/pbsuite/honey/bakH.py-951-        r, o, e = exe("phrap %s -minmatch 6 -minscore 20" % (foutreads.name), timeout=3)
##############################################
pbsuite-15.8.24+dfsg/.pc/blasr-5.patch/pbsuite/honey/bakH.py-961-        if len(results) == 0:
pbsuite-15.8.24+dfsg/.pc/blasr-5.patch/pbsuite/honey/bakH.py:962:            logging.warning('no asm made ' + self.name)
pbsuite-15.8.24+dfsg/.pc/blasr-5.patch/pbsuite/honey/bakH.py-963-            return [] #here is where I'd like to add just the no-consensus spot
##############################################
pbsuite-15.8.24+dfsg/.pc/blasr-5.patch/pbsuite/honey/bakH.py-970-        blasr(foutreads.name, foutreads.name + ".contigs", format="-m 5", nproc=1, outname=alignOut.name)
pbsuite-15.8.24+dfsg/.pc/blasr-5.patch/pbsuite/honey/bakH.py:971:        # elif no asm and consensus only (faster)
pbsuite-15.8.24+dfsg/.pc/blasr-5.patch/pbsuite/honey/bakH.py-972-        
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/Honey.py-22-     force      Given a BedFile of predicted variants, force search for matching
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/Honey.py:23:     asm        Assemble reads around a variant and remap contigs to a reference
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/Honey.py-24-     cpxres     Complex multi-break-point resolution (beta)
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/bakH.py-949-        #run phrap
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/bakH.py:950:        #if asm -- consensus only 
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/bakH.py-951-        r, o, e = exe("phrap %s -minmatch 6 -minscore 20" % (foutreads.name), timeout=3)
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/bakH.py-961-        if len(results) == 0:
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/bakH.py:962:            logging.warning('no asm made ' + self.name)
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/bakH.py-963-            return [] #here is where I'd like to add just the no-consensus spot
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/bakH.py-970-        blasr(foutreads.name, foutreads.name + ".contigs", format="-m 5", nproc=1, outname=alignOut.name)
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/bakH.py:971:        # elif no asm and consensus only (faster)
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/bakH.py-972-        
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-217-        #Fetch,
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py:218:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-219-        reads = {}
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-257-        self.result = self.__assemble(reads)
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py:258:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-259-        return self.result
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-331-        #Fetch,
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py:332:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-333-        reads = []
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-352-        self.result = self.__assemble(reads)
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py:353:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-354-        return self.result
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-481-        #Fetch,
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py:482:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-483-        reads = []
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-506-        self.result = self.__assemble()
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py:507:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-508-        return self.result
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-588-        #Fetch,
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py:589:        logging.info("asm task groupid=%s start" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-590-        reads = []
##############################################
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-617-        
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py:618:        logging.info("asm task groupid=%s finish" % (self.data.name))
pbsuite-15.8.24+dfsg/.pc/2to3.patch/pbsuite/honey/massivePhrap.py-619-        return self.result