heatitup-complete 0.5.4.0 → 0.5.4.1

raw patch · 3 files changed

+14/−9 lines, 3 files

Files

• heatitup-complete.cabal +1/−1
• src/Merge.hs +2/−3
• src/Utility.hs +11/−5

@@ -1,5 +1,5 @@ name:                heatitup-complete-version:             0.5.4.0+version:             0.5.4.1 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

@@ -88,7 +88,7 @@ -- supplementary alignments. mergePair :: Fill -> [BamRow] -> Maybe BamRow mergePair fill xs =-    case filter (not . isSupplementary) xs of+    case filter valid xs of         []  -> Nothing         [x] -> Just x         [BamRow left, BamRow right] ->@@ -103,8 +103,7 @@     posSeq xs = ( either error (Position . fst) . T.decimal $ xs !! 3                 , Sequence $ xs !! 9                 )-    isSupplementary =-        (== "1") . drop 11 . decodeSAMFlag . read . T.unpack . (!! 1) . unBamRow+    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 -- (samtools sort -n).

@@ -15,15 +15,15 @@     , fastaToMap     , getMatchMap     , nub'-    , decodeSAMFlag+    , checkSamFlag     ) where  -- Standard+import Data.Bits ((.&.)) import Data.Bool import Data.Char import Data.Maybe import Data.Monoid-import Numeric import qualified Data.ByteString.Char8 as B import qualified Data.Map.Strict as Map import qualified Data.Set as Set@@ -31,6 +31,7 @@ -- Cabal import qualified Control.Foldl as Fold import qualified Data.Text as T+import qualified Data.Text.Read as T import Data.Fasta.Text import Safe import Turtle.Line@@ -100,6 +101,11 @@ nub' :: (Eq a, Ord a) => [a] -> [a] nub' = Set.toList . Set.fromList --- | Decode a SAM flag into the bit representation (as a string).-decodeSAMFlag :: Int -> String-decodeSAMFlag x = showIntAtBase 2 intToDigit x ""+-- | Decode a SAM flag to check a property of the read.+checkSamFlag :: Int -> BamRow -> Bool+checkSamFlag property = (== property)+                      . (.&.) property+                      . either error fst+                      . T.decimal+                      . (!! 1)+                      . unBamRow