heatitup-complete 0.5.3.3 → 0.5.4.0

raw patch · 2 files changed

+23/−2 lines, 2 files

Files

• app/Main.hs +21/−0
• heatitup-complete.cabal +2/−2

@@ -31,6 +31,7 @@ import qualified Data.Text as T import qualified Data.Vector as V import qualified Options.Applicative as O+import Safe (headMay) import Turtle import Turtle.Line @@ -52,6 +53,7 @@                        , refField              :: Int                        , posField              :: Maybe Int                        , ignoreField           :: Maybe Int+                       , ignoreChar            :: Maybe String                        , inputMinSize          :: Int                        , gaussWindow           :: Int                        , gaussTime             :: Double@@ -165,6 +167,13 @@                    \ and thus helps remove false positives."           )         )+      <*> O.optional ( O.strOption+          ( O.long "ignore-char"+         <> O.metavar "[Nothing or NonAssembly CHAR] | CHAR"+         <> O.help "Character to ignore, useful for gaps.\+                   \ Defaults to nothing or the character used in NonAssembly."+          )+        )       <*> O.option O.auto           ( O.long "min-size"          <> O.short 's'@@ -488,6 +497,17 @@ runFindDuplication opts streamIn =     inproc "heatitup" commandList streamIn   where+    ignoreCharArg (NonAssembly c) = Just+                                  . ("--ignore-char" :)+                                  . (\x -> [[x]])+                                  . fromMaybe c+                                  . (=<<) headMay+                                  . ignoreChar+                                  $ opts+    ignoreCharArg _ = fmap (("--ignore-char" :) . (\x -> [[x]]))+                    . (=<<) headMay+                    . ignoreChar+                    $ opts     commandList =         fmap T.pack             . concat@@ -501,6 +521,7 @@               , Just ["--reference-field", show . refField $ opts]               , fmap (("--position-field" :) . (:[]) . show) . posField $ opts               , fmap (("--ignore-field" :) . (:[]) . show) . ignoreField $ opts+              , ignoreCharArg $ preprocessType opts               , Just ["--min-size", show . inputMinSize $ opts]               , Just ["--gaussian-window", show . gaussWindow $ opts]               , Just ["--gaussian-time", show . gaussTime $ opts]

@@ -1,5 +1,5 @@ name:                heatitup-complete-version:             0.5.3.3+version:             0.5.4.0 synopsis:            Find and annotate ITDs with assembly or read pair joining. description:         Find and annotate ITDs with assembly or read pair joining using suffix trees and characterize the exogenous segments within the spacer using heat diffusion. homepage:            http://github.com/GregorySchwartz/heatitup-complete#readme@@ -7,7 +7,7 @@ license-file:        LICENSE author:              Gregory W. Schwartz maintainer:          gsch@pennmedicine.upenn.edu-copyright:           Copyright: (c) 2018 Gregory W. Schwartz+copyright:           Copyright: (c) 2019 Gregory W. Schwartz category:            Bioinformatics build-type:          Simple -- extra-source-files: