heatitup-complete 0.5.4.1 → 0.5.5.0

raw patch · 2 files changed

+7/−2 lines, 2 files

Files

• heatitup-complete.cabal +1/−1
• src/Merge.hs +6/−1

@@ -1,5 +1,5 @@ name:                heatitup-complete-version:             0.5.4.1+version:             0.5.5.0 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

@@ -23,6 +23,7 @@  -- Cabal import Control.Lens+import qualified Data.Fasta.Text as F import qualified Data.Text as T import qualified Data.Text.Read as T import Safe@@ -101,8 +102,12 @@         xs -> error ("Too many mate pairs (even after supplementary removal) for: " <> show xs)   where     posSeq xs = ( either error (Position . fst) . T.decimal $ xs !! 3-                , Sequence $ xs !! 9+                , Sequence . revComplCheck (BamRow xs) $ xs !! 9                 )+    revComplCheck row fSeq =+      if checkSamFlag 16 row+        then (F.fastaSeq . F.revCompl $ F.FastaSequence "" fSeq)+        else fSeq     valid x = not (checkSamFlag 2048 x) && not (checkSamFlag 256 x)  -- Make sure not supplementary nor not primary  -- | Merge all mate pairs. Assumes that the lines are sorted by mate pair already