From 486af6fa2a50a72d1490c86bd2179e532ef0fe62 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 6 Feb 2025 18:18:14 +0100
Subject: [PATCH] Can now process files given as command-line args.
---
README.md | 8 +++++++-
app/Main.hs | 21 ++++++++++++++++++++-
remove-duplicates-from-sorted-fastq.cabal | 2 +-
3 files changed, 28 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index 4fa9856..6cedfda 100644
--- a/README.md
+++ b/README.md
@@ -42,4 +42,10 @@ fastq file provided in the `test` directory:
fastq-sort -s test/example.fq | remove-duplicates-from-sorted-fastq > test/dedup.fq
-The resulting `test/dedup.fq` should be identical to `test/dedup_expected.fq`.
+This can also be achieved in two steps:
+
+ fastq-sort -s test/example.fq > test/sorted.fq
+ remove-duplicates-from-sorted-fastq test/sorted.fq > test/dedup.fq
+
+In both cases, the resulting `test/dedup.fq` should be identical to
+`test/dedup_expected.fq`.
diff --git a/app/Main.hs b/app/Main.hs
index b635c63..5e67644 100644
--- a/app/Main.hs
+++ b/app/Main.hs
@@ -1,6 +1,7 @@
{-# LANGUAGE OverloadedStrings #-}
module Main where
+import System.Environment (getArgs)
-- For more efficient text manipulation
import qualified Data.ByteString.Lazy.Char8 as C
@@ -66,5 +67,23 @@ text-formatted fastq records into a single text.
C.interact deals with the IO interaction, i.e. taking
text from the outside world and returning text to it.
-}
+processStdin :: IO ()
+processStdin = C.interact (C.concat . processLines . C.lines)
+
+processPath :: String -> IO ()
+processPath path = do
+ fileContent <- (C.readFile path)
+ C.putStr ((C.concat . processLines . C.lines) fileContent)
+
+selectAction :: [String] -> IO ()
+selectAction [] = processStdin
+selectAction (path : []) = do
+ processPath path
+selectAction (path : nextArgs) = do
+ processPath path
+ selectAction nextArgs
+
main :: IO ()
-main = C.interact (C.concat . processLines . C.lines)
+main = do
+ args <- getArgs
+ selectAction args
diff --git a/remove-duplicates-from-sorted-fastq.cabal b/remove-duplicates-from-sorted-fastq.cabal
index b94734b..dd57206 100644
--- a/remove-duplicates-from-sorted-fastq.cabal
+++ b/remove-duplicates-from-sorted-fastq.cabal
@@ -16,7 +16,7 @@ name: remove-duplicates-from-sorted-fastq
-- PVP summary: +-+------- breaking API changes
-- | | +----- non-breaking API additions
-- | | | +--- code changes with no API change
-version: 0.1.0.0
+version: 0.1.1.0
-- A short (one-line) description of the package.
-- synopsis:
--
GitLab