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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