heatitup (empty) → 0.5.3.3
raw patch · 13 files changed
+2312/−0 lines, 13 filesdep +basedep +bytestringdep +bytestring-showsetup-changed
Dependencies added: base, bytestring, bytestring-show, cassava, colour, containers, diagrams-core, diagrams-html5, diagrams-lib, diagrams-pgf, diagrams-rasterific, diagrams-svg, edit-distance, fasta, heatitup, lens, optparse-applicative, pipes, pipes-bytestring, pipes-csv, safe, string-similarity, stringsearch, suffixtree, vector
Files
- LICENSE +674/−0
- Setup.hs +2/−0
- app/Main.hs +571/−0
- heatitup.cabal +75/−0
- src/Classify.hs +23/−0
- src/Diffusion.hs +48/−0
- src/Load.hs +35/−0
- src/Plot.hs +111/−0
- src/Print.hs +72/−0
- src/Repeated.hs +208/−0
- src/Spacer.hs +233/−0
- src/Types.hs +119/−0
- src/Utility.hs +141/−0
+ LICENSE view
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+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ app/Main.hs view
@@ -0,0 +1,571 @@+{- heatitup+Gregory W. Schwartz++Find duplications a sequence.+-}++{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE PartialTypeSignatures #-}+{-# OPTIONS_GHC -fno-warn-partial-type-signatures #-}++module Main where++-- Standard+import Control.Monad+import Data.Char+import Data.Maybe+import Data.Bool+import Data.Semigroup ((<>))+import qualified Data.Map.Strict as Map+import qualified Data.Set as Set+import qualified System.IO as IO++-- Cabal+import Control.Lens+import Data.Colour.SRGB (sRGB24read)+import Data.Fasta.ByteString+import Diagrams.TwoD.Size (mkWidth, mkHeight)+import Options.Applicative+import Pipes+import Pipes.Csv+import Safe+import Diagrams.TwoD.Size+import Diagrams.Backend.PGF (renderPGF, PGF)+import Diagrams.Backend.SVG (renderSVG, SVG)+import Diagrams.Backend.Html5 (renderHtml5, Html5)+import Diagrams.Backend.Rasterific (renderRasterific, Rasterific)+import qualified Diagrams.Prelude as D+import qualified Data.ByteString.Char8 as C+import qualified Data.Vector as V+import qualified Pipes.ByteString as PB+import qualified Pipes.Prelude as P++-- Local+import Types+import Utility+import Load+import Repeated+import Spacer+import Classify+import Plot+import Print++-- | Command line arguments+data Options = Options { input :: Maybe String+ , spacerFlag :: Bool+ , refInput :: Maybe String+ , blacklistInput :: Maybe String+ , output :: Maybe String+ , outputPlot :: Maybe String+ , outputSize :: Double+ , outputLabel :: String+ , refField :: Int+ , posField :: Maybe Int+ , ignoreField :: Maybe Int+ , inputMinSize :: Int+ , gaussWindow :: Int+ , gaussTime :: Double+ , gaussThreshold :: Double+ , inputMinMut :: Maybe Int+ , inputDistance :: Int+ , refCheckBlacklistFlag :: Bool+ , refRecBlacklistFlag :: Bool+ , minRichness :: Int+ , inputColorDupL :: String+ , inputColorDupR :: String+ , inputColorMut :: String+ , inputColorSpacer :: String+ , inputColorBackground :: String+ , inputColorForeground :: String+ }++-- | Command line options+options :: Parser Options+options = Options+ <$> optional ( strOption+ ( long "input"+ <> short 'i'+ <> metavar "FILE"+ <> help "The input file"+ )+ )+ <*> switch+ ( long "spacer"+ <> short 's'+ <> help "Whether to characterize the spacer. Requires\+ \ reference-input and matching labels for the input and\+ \ reference-input to compare."+ )+ <*> optional ( strOption+ ( long "reference-input"+ <> short 'I'+ <> metavar "[Nothing] | FILE"+ <> help "The input file containing the reference sequences to compare\+ \ to. The first entry in the field must be the accession and\+ \ match the requested field from reference-field for the\+ \ input. With no supplied file, no spacer will be annotated."+ )+ )+ <*> optional ( strOption+ ( long "blacklist-input"+ <> short 'b'+ <> metavar "[Nothing] | FILE"+ <> help "The input fasta file containing possible false positives --\+ \ sequences which may be duplicate nucleotides in the\+ \ reference sequence."+ )+ )+ <*> optional ( strOption+ ( long "output"+ <> short 'o'+ <> metavar "FILE"+ <> help "The output file"+ )+ )+ <*> optional ( strOption+ ( long "output-plot"+ <> short 'O'+ <> metavar "FILE"+ <> help "The output file for the plot. Each new plot gets a new number\+ \ on it: output_1.svg, output_2.svg, etc. Each plot uses the\+ \ first entry in the fasta header as the label. If FILE is\+ \ HEADER (i.e. HEADER.pdf), uses the first entry in the fasta\+ \ header as FILE along with the number. Supports html, png,\+ \ tif, jpg, bmp, svg, and pdf. svg may render text differently\+ \ in different situations, and pdf uses LaTeX for rendering\+ \ and may also have issues if reads are too long, but the\+ \ options are there and may be fixed in future releases."+ )+ )+ <*> option auto+ ( long "output-size"+ <> short 'u'+ <> metavar "SIZE"+ <> value 20+ <> help "([20] | DOUBLE) The size of the sequence image output."+ )+ <*> strOption+ ( long "label"+ <> short 'l'+ <> metavar "STRING"+ <> value ""+ <> help "The label to use in the label column for the output"+ )+ <*> option auto+ ( long "reference-field"+ <> short 'f'+ <> metavar "[1] | INT"+ <> value 1+ <> help "The field in each input header that contains the reference\+ \ accession number to compare to. Results in an out of bounds\+ \ if this field does not exist."+ )+ <*> optional ( option auto+ ( long "position-field"+ <> short 'p'+ <> metavar "[Nothing] | INT"+ <> help "The field in each input header that contains the starting\+ \ position of the read. Added to the annotations. Results\+ \ in out of bounds if this field does not exist."+ )+ )+ <*> optional ( option auto+ ( long "ignore-field"+ <> short 'g'+ <> metavar "[Nothing] | INT"+ <> help "The field in each input header that contains a 0 or a 1:\+ \ 0 means to ignore this read (assign as Normal) and 1\+ \ means to find a duplication in this read.\+ \ Used for reads where there is known to be no duplication\+ \ and thus helps remove false positives."+ )+ )+ <*> option auto+ ( long "min-size"+ <> short 'S'+ <> metavar "[15] | INT"+ <> value 15+ <> help "The minimum size of a duplication"+ )+ <*> option auto+ ( long "gaussian-window"+ <> short 'w'+ <> metavar "[3] | Double"+ <> value 3+ <> help "The window for the discrete gaussian kernel atypical spacer\+ \ determination"+ )+ <*> option auto+ ( long "gaussian-time"+ <> short 't'+ <> metavar "[2] | Double"+ <> value 2+ <> help "The time for the discrete gaussian kernel atypical spacer\+ \ determination"+ )+ <*> option auto+ ( long "gaussian-threshold"+ <> short 'T'+ <> metavar "[0.4] | Double"+ <> value 0.4+ <> help "The cutoff to be considered a mutation for the discrete\+ \ gaussian kernel atypical spacer determination"+ )+ <*> optional ( option auto+ ( long "min-mutations"+ <> short 'm'+ <> metavar "INT"+ <> help "The minimum number of nucleotides between mutations"+ )+ )+ <*> option auto+ ( long "levenshtein-distance"+ <> short 'L'+ <> metavar "[2] | INT"+ <> value 2+ <> help "The minimum Levenshtein distance to the false positive\+ \ checker. If the distance to the false positive string\+ \ is less than or equal to this number,\+ \ the duplication is considered\+ \ a false positive. Compares candidates against each sequence\+ \ in --blacklist-input"+ )+ <*> switch+ ( long "reference-check-blacklist"+ <> short 'c'+ <> help "Whether to use the reference as a blacklist in addition to\+ \ the supplied blacklist. That is, we check if the duplication\+ \ can be found twice or more in the reference input."+ )+ <*> switch+ ( long "reference-recursive-blacklist"+ <> short 'r'+ <> help "Whether to use the reference as a recursive\+ \ blacklist in addition to\+ \ the supplied blacklist. That is, the reference sequences\+ \ are inputed with the same parameters (except distance, which\+ \ here is 0)\+ \ to the duplication finder, and those duplications found are\+ \ added to the blacklist. This process is recursive, executed\+ \ until no more duplications are found in the reference.\+ \ Beware, too many blacklist entries can slow down the finder\+ \ significantly, as each blacklist entry is compared with each\+ \ candidate."+ )+ <*> option auto+ ( long "min-richness"+ <> short 'R'+ <> metavar "[1] | INT"+ <> value 1+ <> help "The minimum nucleotide richness (number of different types of\+ \ nucleotides) allowed in the duplication to be considered\+ \ real. Useful if the user knows that a sequence like\+ \ \"TTTTTTTTCTTTTTTTTC\" is not likely to be real."+ )+ <*> strOption+ ( long "color-left-duplication"+ <> metavar "[#a6cae3] | COLOR"+ <> help "The color of the left side of the repeated sequence."+ <> value "#a6cae3"+ )+ <*> strOption+ ( long "color-right-duplication"+ <> metavar "[#b0de8a] | COLOR"+ <> help "The color of the right side of the repeated sequence."+ <> value "#b0de8a"+ )+ <*> strOption+ ( long "color-difference"+ <> metavar "[#1978b3] | COLOR"+ <> help "The color of discrepancies between the left and right side of\+ \ the duplication."+ <> value "#1978b3"+ )+ <*> strOption+ ( long "color-spacer"+ <> metavar "[#fdbd6e] | COLOR"+ <> help "The color of the exogenous nucleotides within the spacer."+ <> value "#fdbd6e"+ )+ <*> strOption+ ( long "color-background"+ <> metavar "[#ffffff] | COLOR"+ <> help "The color of the background."+ <> value "#ffffff"+ )+ <*> strOption+ ( long "color-foreground"+ <> metavar "[#000000] | COLOR"+ <> help "The color of the foreground."+ <> value "#000000"+ )++plotITDM :: Options+ -> Colors+ -> (Int, (ITD, FastaSequence))+ -> IO (ITD, FastaSequence)+plotITDM opts colors (!count, (!itd, !fs)) = do+ let fileType = fmap ( fmap toLower+ . reverse+ . takeWhile (/= '.')+ . reverse+ )+ . outputPlot+ $ opts+ firstField =+ maybe+ "output"+ (fmap (\x -> if x == '.' || x == '/' then '_' else x) . C.unpack)+ . headMay+ . C.split '|'+ . fastaHeader+ $ fs+ savefile = (++ "_" ++ show count ++ "." ++ fromJust fileType)+ . (\x -> case reverse . drop 1 . dropWhile (/= '.') . reverse $ x of+ "HEADER" -> firstField+ y -> y+ )+ . fromJust+ . outputPlot+ $ opts+ size = outputSize opts++ case fileType of+ (Just "pdf") -> renderPGF savefile (mkHeight size)+ . (\x -> plotITD colors fs itd x :: D.Diagram PGF)+ . Query+ . fastaSeq+ $ fs+ (Just "svg") -> renderSVG savefile (mkHeight size)+ . (\x -> plotITD colors fs itd x :: D.Diagram SVG)+ . Query+ . fastaSeq+ $ fs+ (Just "html") -> renderHtml5 savefile (mkHeight size)+ . (\x -> plotITD colors fs itd x :: D.Diagram Html5)+ . Query+ . fastaSeq+ $ fs+ (Just "png") -> renderRasterific savefile (mkHeight size)+ . (\x -> plotITD colors fs itd x :: D.Diagram Rasterific)+ . Query+ . fastaSeq+ $ fs+ (Just "tif") -> renderRasterific savefile (mkHeight size)+ . (\x -> plotITD colors fs itd x :: D.Diagram Rasterific)+ . Query+ . fastaSeq+ $ fs+ (Just "jpg") -> renderRasterific savefile (mkHeight size)+ . (\x -> plotITD colors fs itd x :: D.Diagram Rasterific)+ . Query+ . fastaSeq+ $ fs+ (Just "bmp") -> renderRasterific savefile (mkHeight size)+ . (\x -> plotITD colors fs itd x :: D.Diagram Rasterific)+ . Query+ . fastaSeq+ $ fs+ (Just x) -> error $ x <> " filetype not supported for output."+ Nothing -> return ()++ return (itd, fs)++getReferenceSeq :: Int -> FastaSequence -> ReferenceMap -> ReferenceSeq+getReferenceSeq field fs = ReferenceSeq+ . fastaSeq+ . fromMaybe ( error+ . (++) "Reference accession field not found in: "+ . C.unpack+ . fastaHeader+ $ fs+ )+ . Map.lookup ( Accession+ . getField field '|'+ $ fs+ )+ . unReferenceMap++-- | Unpack a longest substring into a string.+unpackSubstring :: LongestSubstring -> String+unpackSubstring = C.unpack . unSubstring . _dupSubstring . unLongestSubstring++-- | Get a blacklist using a recursive method on the reference sequences. That+-- is, repeatedly exhaust all possibly repeats in the reference sequences.+-- Slower than the reference check if there are lots of sequences in the+-- reference.+refRecBlacklist :: RepeatConfig -> [FastaSequence] -> Blacklist+refRecBlacklist !tempConfig fss =+ case catMaybes longestList of+ [] -> _blacklist tempConfig+ xs -> refRecBlacklist+ ( over blacklist ( Blacklist+ . Set.union ( Set.fromList+ . fmap unpackSubstring+ $ xs+ )+ . unBlacklist+ ) tempConfig+ )+ . catMaybes+ . zipMaybe longestList+ $ fss+ where+ longestList = fmap+ ( longestRepeatedSubstringMutations tempConfig []+ . Query+ . fastaSeq+ )+ fss++mainFunc :: Options -> IO ()+mainFunc opts = do+ hIn <- case input opts of+ Nothing -> return IO.stdin+ (Just x) -> IO.openFile x IO.ReadMode+ hOut <- case output opts of+ Nothing -> return IO.stdout+ (Just x) -> IO.openFile x IO.WriteMode++ refMap <- case refInput opts of+ Nothing -> return Nothing+ (Just x) -> IO.withFile x IO.ReadMode $ \hRefIn ->+ fmap (Just . toReferenceMap (Field 1))+ . readFasta+ $ hRefIn++ suppliedBlacklist <-+ case blacklistInput opts of+ Nothing -> return . Blacklist $ Set.empty+ (Just x) -> IO.withFile x IO.ReadMode $ \hRefIn ->+ fmap (Blacklist . Set.fromList . fmap (C.unpack . fastaSeq))+ . readFasta+ $ hRefIn++ let colors = Colors { _colorDupL = sRGB24read . inputColorDupL $ opts+ , _colorDupR = sRGB24read . inputColorDupR $ opts+ , _colorMut = sRGB24read . inputColorMut $ opts+ , _colorSpacer =+ sRGB24read . inputColorSpacer $ opts+ , _colorBackground =+ sRGB24read . inputColorBackground $ opts+ , _colorForeground =+ sRGB24read . inputColorForeground $ opts+ }+ tempConfig = RepeatConfig+ { _blacklist = suppliedBlacklist+ , _refMap = refMap+ , _richness = Richness . minRichness $ opts+ , _distance = Distance 0+ , _alphabet = "ATCG"+ , _minSize = MinSize . inputMinSize $ opts+ , _minMut = fmap MinMut . inputMinMut $ opts+ , _refCheckFlag = refCheckBlacklistFlag opts+ }+ finalBlacklist =+ if refRecBlacklistFlag opts+ then refRecBlacklist tempConfig+ . Map.elems+ . unReferenceMap+ . fromMaybe (error "No reference supplied.")+ $ refMap+ else suppliedBlacklist+ config = set distance (Distance . inputDistance $ opts)+ . set blacklist finalBlacklist+ $ tempConfig+ getDup fs = ( join+ . fmap ( longestRepeatedSubstringMutations config []+ . Query+ . fastaSeq+ )+ . maybe (Just fs) (flip ignore fs)+ . ignoreField+ $ opts+ , fs+ )+ getSpace Nothing (!dup, !fs) =+ ( ITD { _duplication = fmap unLongestSubstring dup+ , _spacer = Nothing+ }+ , fs+ )+ getSpace (Just rMap) (!dup, !fs) =+ ( ITD { _duplication = fmap unLongestSubstring dup+ , _spacer =+ join+ . fmap ( flip ( getSpacer+ (Window $ gaussWindow opts)+ (Time $ gaussTime opts)+ (Threshold $ gaussThreshold opts)+ refSeq+ )+ (Query . fastaSeq $ fs)+ . unLongestSubstring+ )+ $ dup+ }+ , fs+ )+ where+ refSeq = getReferenceSeq (refField opts) fs rMap+ getClass (!itd, !fs) = (classifyITD itd, itd, fs)+ addPos fs =+ maybe (Position 1) (\ x -> Position+ . read+ . C.unpack+ . fromMaybe ( error+ $ "Position field out of bounds (use another field number): "+ <> (C.unpack . fastaHeader $ fs)+ )+ . (flip atMay (x - 1))+ . C.split '|'+ . fastaHeader $ fs+ )+ . posField+ $ opts+ printRow (!c, !itd, !fs) =+ printITD+ (Label . C.pack . outputLabel $ opts)+ (addPos fs)+ fs+ c+ itd+ headerOrder = V.fromList [ C.pack "label"+ , C.pack "fHeader"+ , C.pack "fSequence"+ , C.pack "dSubstring"+ , C.pack "dLocations"+ , C.pack "dMutations"+ , C.pack "sSubstring"+ , C.pack "sLocation"+ , C.pack "sOtherLocations"+ , C.pack "classification"+ ]++ runEffect $ ( ( P.zip (Pipes.each [1..])+ ( pipesFasta (PB.fromHandle hIn)+ >-> P.map ( getSpace ( bool Nothing refMap+ $ spacerFlag opts+ )+ . getDup+ )+ )+ )+ >-> P.mapM (plotITDM opts colors)+ >-> P.map (printRow . getClass)+ >-> encodeByName headerOrder+ )+ >-> PB.toHandle hOut++ -- Finish up by closing file if written+ unless (null . input $ opts) (IO.hClose hIn)+ unless (null . output $ opts) (IO.hClose hOut)++main :: IO ()+main = execParser opts >>= mainFunc+ where+ opts = info (helper <*> options)+ ( fullDesc+ <> progDesc "Finds duplications in a sequence"+ <> header "heatitup, Gregory W. Schwartz" )
+ heatitup.cabal view
@@ -0,0 +1,75 @@+name: heatitup+version: 0.5.3.3+synopsis: Find and annotate ITDs.+description: Find and annotate ITDs using suffix trees and characterize the exogenous segments within the spacer using heat diffusion.+homepage: http://github.com/GregorySchwartz/heatitup#readme+license: GPL-3+license-file: LICENSE+author: Gregory W. Schwartz+maintainer: gsch@pennmedicine.upenn.edu+copyright: 2018 Gregory W. Schwartz+category: Bioinformatics+build-type: Simple+-- extra-source-files:+cabal-version: >=1.10++library+ hs-source-dirs: src+ exposed-modules: Types+ , Utility+ , Load+ , Repeated+ , Diffusion+ , Spacer+ , Classify+ , Plot+ , Print+ build-depends: base >= 4.7 && < 5+ , bytestring+ , bytestring-show+ , cassava+ , colour+ , containers+ , diagrams-lib+ , edit-distance+ , fasta+ , lens+ , pipes+ , pipes-bytestring+ , pipes-csv+ , safe+ , string-similarity+ , stringsearch+ , suffixtree+ , vector+ ghc-options: -O2+ default-language: Haskell2010++executable heatitup+ hs-source-dirs: app+ main-is: Main.hs+ ghc-options: -threaded -rtsopts -O2+ build-depends: base+ , heatitup+ , bytestring+ , colour+ , containers+ , diagrams-core+ , diagrams-lib+ , diagrams-pgf+ , diagrams-svg+ , diagrams-html5+ , diagrams-rasterific+ , fasta+ , lens+ , optparse-applicative+ , pipes+ , pipes-bytestring+ , pipes-csv+ , safe+ , vector+ default-language: Haskell2010++source-repository head+ type: git+ location: https://github.com/githubuser/heatitup
+ src/Classify.hs view
@@ -0,0 +1,23 @@+{- Classify+Gregory W. Schwartz++Classify an ITD.+-}++module Classify+ ( classifyITD+ ) where++-- Standard++-- Cabal++-- Local+import Types++-- | Classify an ITD+classifyITD :: ITD -> Classification+classifyITD (ITD { _duplication = Nothing }) = Normal+classifyITD (ITD { _spacer = Nothing}) = Typical+classifyITD (ITD { _spacer = (Just s)}) =+ if not . null . _spacerOtherLocations $ s then Atypical else Typical
+ src/Diffusion.hs view
@@ -0,0 +1,48 @@+{- Diffusion+Gregory W. Schwartz++Collections the functions pertaining to the discrete general diffusion+equation, or the discrete Gaussian kernel+-}++{-# LANGUAGE BangPatterns #-}++module Diffusion+ ( diffuse+ , mutationSignal+ ) where++-- Standard+import Data.Maybe++-- Cabal+import qualified Data.Vector as V+import qualified Data.ByteString.Char8 as C++-- Local+import Types+import Utility++-- | Diffuse a 1 dimensional discrete signal+diffuse :: Window -> Time -> Signal -> Signal+diffuse _ _ (Signal []) = Signal []+diffuse (Window w) (Time t) (Signal xs) = Signal . V.toList . V.imap go $ vec+ where+ vec = V.fromList xs+ go i x =+ sum+ . map ( \n -> (* g (fromIntegral n))+ . fromMaybe 0+ . (V.!?) vec+ . fromIntegral+ $ i - n+ )+ $ [(- w) .. w]+ g n = (1 / (sqrt (2 * pi * t))) * (exp ((- n ^ 2) / (2 * t)))++-- | Convert a hamming comparison to a signal+mutationSignal :: C.ByteString -> Substring -> Signal+mutationSignal base = Signal+ . fmap (\x -> if x then 0 else 1)+ . hammingList base+ . unSubstring
+ src/Load.hs view
@@ -0,0 +1,35 @@+{- Print+Gregory W. Schwartz++Collections the functions pertaining to the loading of fasta files.+-}++module Load+ ( readFasta+ , toReferenceMap+ ) where++-- Standard+import qualified Data.Map.Strict as Map+import qualified System.IO as IO++-- Cabal+import Pipes+import qualified Pipes.Prelude as P+import qualified Pipes.ByteString as PB+import Data.Fasta.ByteString++-- Local+import Types++-- | Load an input fasta file.+readFasta :: IO.Handle -> IO [FastaSequence]+readFasta hRefIn =+ runEffect $ P.toListM . pipesFasta . PB.fromHandle $ hRefIn++-- | Convert a list of reference sequences to a map of their accessions+toReferenceMap :: Field -> [FastaSequence] -> ReferenceMap+toReferenceMap (Field x) =+ ReferenceMap+ . Map.unions+ . fmap (\fs -> Map.singleton (Accession . getField x '|' $ fs) fs)
+ src/Plot.hs view
@@ -0,0 +1,111 @@+{- Plot+Gregory W. Schwartz++Collections the functions pertaining to plotting the sequence.+-}++{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE FlexibleContexts #-}+{-# LANGUAGE GADTs #-}+{-# LANGUAGE PartialTypeSignatures #-}+{-# OPTIONS_GHC -fno-warn-partial-type-signatures #-}++module Plot+ ( plotITD+ ) where++-- Standard+import Data.Maybe+import Data.List++-- Cabal+import qualified Data.ByteString.Char8 as C+import Data.Colour.SRGB (sRGB24read)+import Diagrams.Prelude+import Data.Fasta.ByteString++-- Local+import Types++foreground colors p (!xs, !ys)+ | p `elem` xs = square 1 # fc (_colorMut colors) # lc (_colorMut colors)+ | p `elem` ys = square 1 # fc (_colorSpacer colors) # lc (_colorSpacer colors)+ | otherwise = mempty++background colors p (!xs, !ys)+ | p `elem` xs = _colorDupL colors+ | p `elem` ys = _colorDupR colors+ | otherwise = _colorBackground colors++plotNucleotide colors nuc mut backG =+ text nuc # fc (_colorForeground colors)+ <> mut+ <> square 1 # fc backG # lc backG++plotITD+ :: _+ => Colors -> FastaSequence -> ITD -> Types.Query -> QDiagram b V2 n Any+plotITD colors fs itd = hcat+ . (:) ( text label+ <> rect (genericLength label) 1 # lw none+ )+ . fmap (uncurry plotNuc)+ . zip (fmap Position [0..])+ . C.unpack+ . unQuery+ where+ label = takeWhile (/= '|') . C.unpack . fastaHeader $ fs+ dupLen = fromMaybe 0+ . fmap (C.length . unSubstring . _dupSubstring)+ . _duplication+ $ itd+ plotNuc p x =+ plotNucleotide+ colors+ (x : [])+ ( foreground colors p ( ( fromMaybe []+ . fmap _dupMutations+ . _duplication+ $ itd+ )+ , ( fromMaybe []+ . fmap _spacerOtherLocations+ . _spacer+ $ itd+ )+ )+ )+ ( background+ colors+ p+ ( fromMaybe ([], [])+ . fmap ( (\[x, y] -> (dupPositions x, dupPositions y))+ . _dupLocations+ )+ . _duplication+ $ itd+ )+ )+ dupPositions (Position x) = fmap Position [x .. x + dupLen - 1]++gruvColors :: String -> Colour Double+gruvColors "background" = sRGB24read "#282828"+gruvColors "foreground" = sRGB24read "#ebdbb2"+gruvColors "black" = sRGB24read "#282828"+gruvColors "darkgrey" = sRGB24read "#928374"+gruvColors "darkred" = sRGB24read "#cc241d"+gruvColors "red" = sRGB24read "#fb4934"+gruvColors "darkgreen" = sRGB24read "#98971a"+gruvColors "green" = sRGB24read "#b8bb26"+gruvColors "darkyellow" = sRGB24read "#d79921"+gruvColors "yellow" = sRGB24read "#fabd2f"+gruvColors "darkblue" = sRGB24read "#458588"+gruvColors "blue" = sRGB24read "#83a598"+gruvColors "brightblue" = sRGB24read "#2e9ef4"+gruvColors "darkmagenta" = sRGB24read "#b16286"+gruvColors "magenta" = sRGB24read "#d3869b"+gruvColors "darkcyan" = sRGB24read "#689d6a"+gruvColors "cyan" = sRGB24read "#8ec07c"+gruvColors "lightgrey" = sRGB24read "#a89984"+gruvColors "white" = sRGB24read "#ebdbb2"
+ src/Print.hs view
@@ -0,0 +1,72 @@+{- Print+Gregory W. Schwartz++Collections the functions pertaining to printing the ITD output.+-}++{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE OverloadedStrings #-}++module Print+ ( printITD+ ) where++-- Standard+import Data.Maybe++-- Cabal+import qualified Data.ByteString.Char8 as C+import qualified Data.ByteString.Lazy.Char8 as CL+import qualified Text.Show.ByteString as CS+import Data.Fasta.ByteString++-- Local+import Types++-- | Put the ITD type in a record to be converted to a csv row+printITD :: Label+ -> Position+ -> FastaSequence+ -> Classification+ -> ITD+ -> PrintITD+printITD (Label l) p fs classification itd =+ PrintITD { label = l+ , fHeader = fastaHeader fs+ , fSequence = fastaSeq fs+ , dSubstring = fromMaybe ""+ . fmap (unSubstring . _dupSubstring)+ . _duplication+ $ itd+ , dLocations = fromMaybe ""+ . fmap (possToString p . _dupLocations)+ . _duplication+ $ itd+ , dMutations = fromMaybe ""+ . fmap (possToString p . _dupMutations)+ . _duplication+ $ itd+ , sSubstring = fromMaybe ""+ . fmap (unSubstring . _spacerSubstring)+ . _spacer+ $ itd+ , sLocation =+ fromMaybe ""+ . fmap (posToString p . _spacerLocation)+ . _spacer+ $ itd+ , sOtherLocations = fromMaybe ""+ . fmap (possToString p . _spacerOtherLocations)+ . _spacer+ $ itd+ , classification = C.pack . show $ classification+ }++-- | Convert a list of positions to a string.+possToString :: Position -> [Position] -> C.ByteString+possToString p = C.intercalate "/" . fmap (posToString p)++-- | Convert a position to a string. Add the starting point of the read+-- (converts to 1 indexed).+posToString :: Position -> Position -> C.ByteString+posToString p = CL.toStrict . CS.show . unPosition . (+ p)
+ src/Repeated.hs view
@@ -0,0 +1,208 @@+{- Repeated+Gregory W. Schwartz++Collections the functions pertaining to finding the longest repeated substring+-}++{-# LANGUAGE BangPatterns #-}++module Repeated+ ( longestRepeatedSubstring+ , longestRepeatedSubstringMutations+ ) where++-- Standard+import Control.Monad+import Data.List+import Data.Maybe+import Data.Ord+import qualified Data.Map as Map+import qualified Data.Set as Set++-- Cabal+import Control.Lens+import Data.ByteString.Search+import Data.Fasta.ByteString+import Safe+import qualified Data.ByteString.Char8 as C+import qualified Data.SuffixTree as ST++-- Local+import Types+import Utility++longestRepeatedSubstringMutations :: RepeatConfig+ -> [Position]+ -> Query+ -> Maybe LongestSubstring+longestRepeatedSubstringMutations config muts q = do+ longest <-+ longestRepeatedSubstring config q++ result <-+ case ( _minMut config+ , getNextLongestF longest, getNextLongestB longest+ ) of+ (Nothing, _, _) -> Just longest+ (_, Nothing, Nothing) -> addMuts longest+ (Just (MinMut mm), forward, backward) ->+ if substringLen (forBackBetter forward backward)+ - substringLen longest < mm+ then addMuts longest+ else longestRepeatedSubstringMutations+ config+ (snd . (forBackQuery forward backward) longest $ q)+ . fst+ $ (forBackQuery forward backward) longest q++ return result+ where+ forBackQuery (Just x) Nothing = newQuery mutateQueryForward+ forBackQuery Nothing (Just x) = newQuery mutateQueryBackward+ forBackQuery (Just forward) (Just backward) =+ if substringLen forward >= substringLen backward+ then newQuery mutateQueryForward+ else newQuery mutateQueryBackward+ forBackBetter Nothing (Just backward) = backward+ forBackBetter (Just forward) Nothing = forward+ forBackBetter (Just forward) (Just backward) =+ if substringLen forward >= substringLen backward+ then forward+ else backward+ addMuts = Just+ . LongestSubstring+ . over dupMutations (++ muts)+ . unLongestSubstring+ substringLen =+ C.length . unSubstring . _dupSubstring . unLongestSubstring+ getNextLongestF l =+ longestRepeatedSubstring config+ . fst+ . newQuery mutateQueryForward l+ $ q+ getNextLongestB l =+ longestRepeatedSubstring config+ . fst+ . newQuery mutateQueryBackward l+ $ q+ newQuery f (LongestSubstring l) = f+ (head . _dupLocations $ l)+ (last . _dupLocations $ l)+ (_dupSubstring l)++-- | Mutate the query by replacing a location in the query with the new+-- substring+mutateQueryForward :: Position+ -> Position+ -> Substring+ -> Query+ -> (Query, [Position])+mutateQueryForward (Position i) (Position j) (Substring s) (Query q) =+ if (i + C.length s >= j) || (j + C.length s >= C.length q)+ then (Query q, [])+ else ( Query . C.concat $ [beginning, new, middle, new, end]+ , [Position $ i + C.length s, Position $ j + C.length s]+ )+ where+ beginning = C.take i q+ middle = C.take (j - (i + C.length s + 1))+ . C.drop (i + C.length s + 1)+ $ q+ end = C.drop (j + C.length s + 1) $ q+ new = C.append s (C.take 1 . C.drop (j + C.length s) $ q)++-- | Mutate the query by replacing a location in the query with the new+-- substring+mutateQueryBackward :: Position+ -> Position+ -> Substring+ -> Query+ -> (Query, [Position])+mutateQueryBackward (Position i) (Position j) (Substring s) (Query q) =+ if i == 0 || j <= i + C.length s - 1+ then (Query q, [])+ else ( Query . C.concat $ [beginning, new, middle, new, end]+ , [Position $ i - 1, Position $ j - 1]+ )+ where+ beginning = C.take (i - 1) q+ middle = C.take (j - (i + C.length s) - 1) . C.drop (i + C.length s) $ q+ end = C.drop (j + C.length s) $ q+ new = C.append (C.take 1 . C.drop (i - 1) $ q) s++-- | Return the longest repeated substring of a list, specifically with an+-- alphabet+longestRepeatedSubstring :: RepeatConfig -> Query -> Maybe LongestSubstring+longestRepeatedSubstring config (Query q) =+ longestNonOverlap (Query q)+ . filter checkThresholds+ . sortBy (comparing snd)+ . substringRankings+ . ST.constructWith (_alphabet config)+ . C.unpack+ . (flip C.snoc '$')+ $ q+ where+ checkThresholds x =+ ((>= (unMinSize $ _minSize config)) . C.length . unSubstring . fst $ x)+ && (checkRichness x)+ && (checkFalsePositive x)+ && (maybe True (checkReference x) . _refMap $ config)+ checkFalsePositive = not+ . itdFalsePositive (_blacklist config) (_distance config)+ . C.unpack+ . unSubstring+ . fst+ checkRichness = (>= (unRichness $ _richness config))+ . getRichness+ . C.unpack+ . unSubstring+ . fst+ checkReference x =+ ((not $ _refCheckFlag config) ||)+ . not+ . any ( (> 1)+ . length+ . nonOverlappingIndices (unSubstring . fst $ x)+ . fastaSeq+ )+ . unReferenceMap++-- | Get the longest non overlapping substring+longestNonOverlap :: Query -> [(Substring, Int)] -> Maybe LongestSubstring+longestNonOverlap q =+ fmap (LongestSubstring . fst)+ . maximumByMay (comparing snd)+ . filter (not . isOverlapping . fst)+ . fmap (\(!s, !n) -> (makeDuplication q s, n))++-- | Get the non overlapping indices of a substring+makeDuplication :: Query -> Substring -> Duplication+makeDuplication (Query q) (Substring s) =+ Duplication+ (Substring s)+ headLastDup+ []+ where+ headLastDup = case [headMay dups, lastMay dups] of+ [Just x, Just y] -> if x == y then [] else [x, y]+ _ -> []+ dups = fmap Position+ . Set.toList+ . Set.fromList+ . flip nonOverlappingIndices q+ $ s++-- | Check if a substring is overlapping+isOverlapping :: Duplication -> Bool+isOverlapping x = null . drop 1 . nub . _dupLocations $ x++-- | Get the deepest substring in a suffix tree+substringRankings :: ST.STree Char -> [(Substring, Int)]+substringRankings = map (over _1 (Substring . C.pack)) . go ([], 0)+ where+ go acc ST.Leaf = [acc]+ go acc@(!x, !n) (ST.Node es) = concatMap (check acc) es+ check acc (_, ST.Leaf) = [acc]+ check (!x, !n) (!p, !tree) =+ go (x ++ ST.prefix p, n + (length . ST.prefix) p) tree
+ src/Spacer.hs view
@@ -0,0 +1,233 @@+{- Spacer+Gregory W. Schwartz++Collections the functions pertaining to finding the spacer in-between+duplications.+-}++{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE TupleSections #-}++module Spacer+ ( getSpacer+ ) where++-- Standard+import Data.List+import Data.Maybe+import Data.Ord+import qualified Data.Set as Set++-- Cabal+import Control.Lens+import Data.ByteString.Search+import Data.List.CommonSubstring+import Safe+import qualified Data.ByteString.Char8 as C++-- Local+import Types+import Utility+import Diffusion++getSpacer :: Window+ -> Time+ -> Threshold+ -> ReferenceSeq+ -> Duplication+ -> Query+ -> Maybe Spacer+getSpacer window+ time+ threshold+ (ReferenceSeq refSeq)+ (Duplication { _dupSubstring = s, _dupLocations = [p1, p2] })+ q+ | C.null . unSubstring $ spacer = Nothing+ | otherwise =+ Just $+ Spacer { _spacerSubstring = spacer+ , _spacerLocation = spacerPos+ , _spacerOtherLocations = otherSpacerPositionsDiffusion+ window+ time+ threshold+ spacerPos+ p1+ p2+ refSeq+ s+ spacer+ }+ where+ spacerPos = Position $ unPosition p1 + dupLen+ spacer = inbetweenSubstring (Length dupLen) p1 p2 q+ dupLen = C.length . unSubstring $ s++-- | Change a string to be identical with the one duplication position+mutateQuery :: Maybe Position -> Substring -> String -> String+mutateQuery Nothing _ _ = []+mutateQuery (Just (Position p)) (Substring s) q =+ concat [beginning, C.unpack s, end]+ where+ beginning = take p q+ end = drop (p + C.length s) $ q++-- | Get the most similar sequence to a base sequence from the left or+-- right substring, along with the base fragment+minHammingLeftRight+ :: C.ByteString+ -> Substring+ -> Substring+ -> Either (Substring, C.ByteString) (Substring, C.ByteString)+minHammingLeftRight base (Substring s) (Substring spacer) =+ either (Left . (Substring leftSeq,)) (Right . (Substring rightSeq,))+ . minimumBy (comparing $ either (hamming leftSeq) (hamming rightSeq))+ . concat+ $ [ fmap (Left . unSubstring) . baseFragments $ leftSeq+ , fmap (Right . unSubstring) . baseFragments $ rightSeq+ ]+ where+ baseFragments xs = fragmentSequenceFiller (Window . C.length $ xs) $ base+ leftSeq = getLeftRightFull LeftP spacer s+ rightSeq = getLeftRightFull RightP spacer s++-- | Get the positions that are different between the spacer and the+-- reference sequence+otherSpacerPositionsDiffusion :: Window+ -> Time+ -> Threshold+ -> Position+ -> Position+ -> Position+ -> C.ByteString+ -> Substring+ -> Substring+ -> [Position]+otherSpacerPositionsDiffusion window+ time+ (Threshold gaussThresh)+ (Position spacerPos)+ (Position p1)+ (Position p2)+ base+ (Substring s)+ (Substring spacer) =+ fmap Position+ . Set.toList+ . Set.intersection (Set.fromList spacerPoss)+ . Set.fromList+ . either (fmap (+ p1)) (fmap (+ spacerPos))+ . over both atypicalPositions+ $ minHamming+ where+ atypicalPositions =+ fmap fst+ . filter snd+ . zip [0..]+ . fmap (>= gaussThresh)+ . unSignal+ . diffusedSeq+ diffusedSeq (joinedSubstring, baseFragment) =+ diffuse window time+ . mutationSignal baseFragment+ $ joinedSubstring+ minHamming = minHammingLeftRight base (Substring s) (Substring spacer)+ spacerPoss = [spacerPos .. p2 - 1]++-- | Get the positions that are different between the spacer and the+-- reference sequence+otherSpacerPositions :: MinSize+ -> Consecutive+ -> Position+ -> Position+ -> Position+ -> C.ByteString+ -> Substring+ -> Substring+ -> [Position]+otherSpacerPositions (MinSize minAtypicalSize)+ consecutive+ (Position spacerPos)+ (Position p1)+ (Position p2)+ base+ (Substring s)+ (Substring spacer)+ | consecutiveSpacerFalsePositive consecutive base+ . Substring+ . getLeftRightPortion LeftP spacer+ $ s+ = []+ | consecutiveSpacerFalsePositive consecutive base+ . Substring+ . getLeftRightPortion RightP spacer+ $ s+ = []+ | otherwise =+ fmap Position+ . Set.toList+ . Set.difference (Set.fromList spacerPoss)+ . Set.intersection (Set.fromList spacerPoss)+ . Set.fromList+ . commonPos+ $ commonStart+ where+ commonPos Nothing = []+ commonPos (Just (Left (Length l))) = [p1 + C.length s - 1 .. p2 - l - 1]+ commonPos (Just (Right (Length l))) = [spacerPos + l .. p2 - 1]+ commonStart = headMay+ . catMaybes+ . fmap ( leftOrRightFound+ (Substring base)+ (Substring spacer)+ (Substring s)+ . Length+ )+ $ [0 .. minLen]+ minLen = if C.length spacer <= minAtypicalSize+ then (-1)+ else C.length spacer - minAtypicalSize+ spacerPoss = [spacerPos .. p2 - 1]++-- | Whether the left or right substring is found in the sequence+leftOrRightFound :: Substring+ -> Substring+ -> Substring+ -> Length+ -> Maybe (Either Length Length)+leftOrRightFound (Substring base) (Substring spacer) (Substring s) (Length l) =+ if C.isInfixOf newString1 base+ then Just . Left . Length $ l+ else if C.isInfixOf newString2 base+ then Just . Right . Length $ l+ else Nothing+ where+ newString1 = C.reverse . C.drop l . C.reverse $ original1+ newString2 = C.drop l original2+ original1 = getLeftRightPortion LeftP spacer s+ original2 = getLeftRightPortion RightP spacer s++-- | Get the string plus a the entirety of another string and+-- concatenate them+getLeftRightFull :: LeftRightPortion+ -> C.ByteString+ -> C.ByteString+ -> C.ByteString+getLeftRightFull LeftP x y = C.append y x+getLeftRightFull RightP x y = C.append x y++-- | Get the string plus a portion (1 / 3) of another string and+-- concatenate them+getLeftRightPortion :: LeftRightPortion+ -> C.ByteString+ -> C.ByteString+ -> C.ByteString+getLeftRightPortion LeftP x y =+ C.append (C.drop (2 * (C.length y `div` 3)) y) x+getLeftRightPortion RightP x y = C.append x . C.take (C.length y `div` 3) $ y++-- | Find the string inbetween two indices of the duplication+inbetweenSubstring :: Length -> Position -> Position -> Query -> Substring+inbetweenSubstring (Length n) (Position x) (Position y) =+ Substring . C.take (y - x - n) . C.drop (x + n) . unQuery
+ src/Types.hs view
@@ -0,0 +1,119 @@+{- Types+Gregory W. Schwartz++Collections the types used in the program+-}++{-# LANGUAGE TemplateHaskell #-}+{-# LANGUAGE GeneralizedNewtypeDeriving #-}+{-# LANGUAGE DeriveGeneric #-}++module Types where++-- Standard+import GHC.Generics+import qualified Data.Map.Strict as Map+import qualified Data.Set as Set++-- Cabal+import Control.Lens+import Data.Csv+import Data.Fasta.ByteString+import qualified Data.ByteString.Char8 as C+import qualified Data.SuffixTree as ST+import Data.Colour.SRGB++-- Local++-- Algebraic+newtype Position = Position { unPosition :: Int }+ deriving (Eq, Show, Num)+newtype LongestSubstring = LongestSubstring+ { unLongestSubstring :: Duplication }+ deriving (Show)+newtype Query = Query { unQuery :: C.ByteString } deriving (Show)+newtype Substring = Substring { unSubstring :: C.ByteString }+ deriving (Eq, Show)+newtype Length = Length Int deriving (Show)+newtype Distance = Distance Int deriving (Show)+newtype Threshold = Threshold Double deriving (Show)+newtype Percent = Percent Double deriving (Show)+newtype Consecutive = Consecutive Int deriving (Show)+newtype Label = Label C.ByteString+newtype MinSize = MinSize { unMinSize :: Int } deriving (Show)+newtype Richness = Richness { unRichness :: Int } deriving (Show)+newtype MinMut = MinMut { unMinMut :: Int } deriving (Show)+newtype MaxMut = MaxMut { unMaxMut :: Int } deriving (Eq, Ord)+newtype Window = Window Int+newtype Signal = Signal { unSignal :: [Double] } deriving (Eq, Ord, Show)+newtype Time = Time Double deriving (Show)+newtype Field = Field Int deriving (Show)+newtype Accession = Accession C.ByteString deriving (Show, Eq, Ord)+newtype Blacklist = Blacklist+ { unBlacklist :: (Set.Set String)+ } deriving (Show)+newtype ReferenceSeq = ReferenceSeq C.ByteString deriving (Show)+newtype ReferenceMap = ReferenceMap+ { unReferenceMap :: (Map.Map Accession FastaSequence)+ } deriving (Show)++data Classification = Typical | Atypical | Normal deriving (Eq, Ord, Read, Show)++data LeftRightPortion = LeftP | RightP deriving (Show)++data Colors = Colors+ { _colorDupL :: Colour Double+ , _colorDupR :: Colour Double+ , _colorMut :: Colour Double+ , _colorSpacer :: Colour Double+ , _colorBackground :: Colour Double+ , _colorForeground :: Colour Double+ } deriving (Generic)++data Duplication = Duplication { _dupSubstring :: Substring+ , _dupLocations :: [Position]+ , _dupMutations :: [Position]+ }+ deriving (Show)+makeLenses ''Duplication++data Spacer = Spacer { _spacerSubstring :: Substring+ , _spacerLocation :: Position+ , _spacerOtherLocations :: [Position]+ }+ deriving (Show)+makeLenses ''Spacer++data ITD = ITD { _duplication :: Maybe Duplication+ , _spacer :: Maybe Spacer+ }+ deriving (Show)+makeLenses ''ITD++data RepeatConfig = RepeatConfig+ { _blacklist :: !Blacklist+ , _refMap :: !(Maybe ReferenceMap)+ , _richness :: !Richness+ , _distance :: !Distance+ , _alphabet :: !(ST.Alphabet Char)+ , _minSize :: !MinSize+ , _minMut :: !(Maybe MinMut)+ , _refCheckFlag :: !Bool+ } deriving (Show)+makeLenses ''RepeatConfig++data PrintITD = PrintITD { label :: C.ByteString+ , fHeader :: C.ByteString+ , fSequence :: C.ByteString+ , dSubstring :: C.ByteString+ , dLocations :: C.ByteString+ , dMutations :: C.ByteString+ , sSubstring :: C.ByteString+ , sLocation :: C.ByteString+ , sOtherLocations :: C.ByteString+ , classification :: C.ByteString+ }+ deriving (Show, Generic)++instance FromNamedRecord PrintITD+instance ToNamedRecord PrintITD
+ src/Utility.hs view
@@ -0,0 +1,141 @@+{- Utility+Gregory W. Schwartz++Collections the functions of general use in the program.+-}++{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE OverloadedStrings #-}++module Utility+ ( zipMaybe+ , fragmentSequence+ , fragmentSequenceFiller+ , hammingList+ , hamming+ , isOverlappingBySubstring+ , itdFalsePositive+ , spacerFalsePositive+ , consecutiveSpacerFalsePositive+ , isConsecutive+ , getRichness+ , ignore+ ) where++-- Standard+import Data.Char+import Data.List+import Data.Maybe+import Data.Monoid+import qualified Data.Foldable as F+import qualified Data.Set as Set++-- Cabal+import qualified Data.ByteString.Char8 as C+import Data.Fasta.ByteString+import Text.EditDistance++-- Local+import Types+++-- | Get the bs that correspond to the Justs in the first list.+zipMaybe :: [Maybe a] -> [b] -> [Maybe b]+zipMaybe xs = zipWith test xs+ where+ test (Just _) x = Just x+ test Nothing x = Nothing++-- | Fragment the sequence by a certain window length+fragmentSequence :: Window -> C.ByteString -> [Substring]+fragmentSequence (Window w) = go []+ where+ go !acc xs+ | C.null xs = acc+ | C.length xs < w = acc+ | otherwise = go (Substring (C.take w xs) : acc)+ . C.drop 1+ $ xs++-- | Fragment the sequence by a certain window length, adding filler+fragmentSequenceFiller :: Window -> C.ByteString -> [Substring]+fragmentSequenceFiller (Window w) =+ go [] . flip C.append filler . C.append filler+ where+ filler = C.replicate (w - 1) '-'+ go !acc xs+ | C.null xs = acc+ | C.length xs < w = acc+ | otherwise = go (Substring (C.take w xs) : acc)+ . C.drop 1+ $ xs++-- | Get the hamming list between two strings+hammingList :: C.ByteString -> C.ByteString -> [Bool]+hammingList xs = C.zipWith (==) xs++-- | Get the hamming distance between two strings+hamming :: C.ByteString -> C.ByteString -> Int+hamming xs = length . filter (not . id) . hammingList xs++-- | Check if positions overlap+isOverlappingByPosition :: Window -> Position -> Position -> Bool+isOverlappingByPosition (Window w) (Position x) (Position y) = abs (x - y) < w++-- | Check if positions overlap at the substring level+isOverlappingBySubstring :: Duplication -> Bool+isOverlappingBySubstring (Duplication s [p1, p2] _) =+ isOverlappingByPosition (Window $ C.length . unSubstring $ s) p1 p2+isOverlappingBySubstring _ =+ error "Multiple locations found when checking for overlap"++-- | Check if a string is a false positive+itdFalsePositive :: Blacklist -> Distance -> String -> Bool+itdFalsePositive (Blacklist blacklist) (Distance d) dup =+ F.any ((<= d) . levenshteinDistance defaultEditCosts dup) blacklist++-- | Check if the spacer is a false positive based on the Levenshtein+-- distance (ignoring the insertions and deletions). The threshold here is+-- a percentage of the spacer with a portion of the duplication (how much+-- of that string differs).+spacerFalsePositive :: Percent -> C.ByteString -> Substring -> Bool+spacerFalsePositive (Percent p) base (Substring s) =+ (<= (p / 100))+ . ( \x -> (fromIntegral x - expectedDistance)+ / (fromIntegral $ C.length s)+ )+ . levenshteinDistance defaultEditCosts (C.unpack base)+ . C.unpack+ $ s+ where+ expectedDistance = fromIntegral $ C.length base - C.length s++-- | Check if the spacer is a false positive based on the Levenshtein+-- distance (ignoring the insertions and deletions). The threshold here is+-- a percentage of the spacer with a portion of the duplication (how much+-- of that string differs).+consecutiveSpacerFalsePositive :: Consecutive+ -> C.ByteString+ -> Substring+ -> Bool+consecutiveSpacerFalsePositive (Consecutive c) base (Substring s) =+ any (not . isConsecutive c . hammingList s . unSubstring)+ . fragmentSequence (Window . C.length $ s)+ $ base++-- | See if any x elements are false and neighboring in a list+isConsecutive :: Int -> [Bool] -> Bool+isConsecutive c = any (\x -> ((>= c) $ length x) && (not $ head x)) . group++-- | Get the richness of a list.+getRichness :: (Eq a, Ord a) => [a] -> Int+getRichness = Set.size . Set.fromList++-- | Check to see if a fasta sequence should be analyzed.+ignore :: Int -> FastaSequence -> Maybe FastaSequence+ignore field fs = case getField field '|' fs of+ "0" -> Nothing+ "1" -> Just fs+ _ -> error+ $ "ignore-field process: neither a 0 nor 1 found at position "+ <> show field