Added missing Haskell program.

trim-t-tail-from-fastq/Haskell/Setup.hs

+import Distribution.Simple
+main = defaultMain

trim-t-tail-from-fastq/Haskell/install.sh

+#!/bin/bash -l
+
+# http://linuxcommand.org/wss0150.php
+PROGNAME=$(basename $0)
+
+function error_exit
+{
+#	----------------------------------------------------------------
+#	Function for exit due to fatal program error
+#		Accepts 1 argument:
+#			string containing descriptive error message
+#	----------------------------------------------------------------
+    echo "${PROGNAME}: ${1:-"Unknown Error"}" 1>&2
+    exit 1
+}
+
+function try_load_gmp_module
+{
+    (module --version 2> /dev/null && module load gmp) || :
+}
+
+if [ $(id -u) = 0 ]
+then
+    # We don't want things to be installed in root's home directory.
+    install="install --local-bin-path /usr/local/bin"
+else
+    install="install"
+fi
+
+config_file="${HOME}/.stack/config.yaml"
+
+stack --version 2> /dev/null \
+    || (echo "loading stack" && module load stack/1.4.0)
+
+if [ "${config_file}" ]
+then
+    stack exec -- ghc --version > /dev/null \
+        || (try_load_gmp_module \
+            && stack setup \
+            && INCLUDE_PATH=$(echo ${CMAKE_INCLUDE_PATH} | tr ":" ",") \
+            && LIBRARY_PATH=$(echo ${CMAKE_LIBRARY_PATH} | tr ":" ",") \
+            && include_config="extra-include-dirs: [${INCLUDE_PATH}]" \
+            && libdir_config="extra-lib-dirs: [${LIBRARY_PATH}]" \
+            && echo "" >> ${config_file} \
+            && echo ${include_config} >> ${config_file} \
+            && echo ${libdir_config} >> ${config_file}) \
+        || error_exit "stack setup failed"
+    make_stack_options () {
+        stack_options=""
+    }
+else
+    stack exec -- ghc --version > /dev/null \
+        || (try_load_gmp_module && stack setup) \
+        || error_exit "stack setup failed"
+    # https://unix.stackexchange.com/a/60690/55127
+    # Delay variable evaluation in order to adapt to loaded libraries
+    make_stack_options () {
+        INCLUDE_PATH=$(echo ${CMAKE_INCLUDE_PATH} | tr ":" ",") \
+        LIBRARY_PATH=$(echo ${CMAKE_LIBRARY_PATH} | tr ":" ",") \
+        stack_options="--extra-include-dirs=${INCLUDE_PATH} --extra-lib-dirs=${LIBRARY_PATH}"
+    }
+fi
+
+# cd ${HOME} to ignore local project stack config
+hlint --version 2> /dev/null \
+    || (try_load_gmp_module && (cd ${HOME} && make_stack_options && stack ${stack_options} ${install} hlint)) \
+    || error_exit "hlint install failed"
+scan --version 2> /dev/null \
+    || (try_load_gmp_module && (cd ${HOME} && make_stack_options && stack ${stack_options} ${install} scan)) \
+    || error_exit "scan install failed"
+doctest --version 2> /dev/null \
+    || (try_load_gmp_module && (cd ${HOME} && make_stack_options && stack ${stack_options} ${install} doctest)) \
+    || error_exit "doctest install failed"
+
+make_stack_options
+stack ${stack_options} build --exec "hlint src/Main.hs" --exec "scan -j False src/Main.hs" --exec "doctest src/Main.hs"
+
+stack ${install}

trim-t-tail-from-fastq/Haskell/src/Main.hs

+{-# LANGUAGE OverloadedStrings #-}
+module Main where
+
+-- For more efficient text manipulation
+-- import qualified Data.ByteString.Lazy.Char8 as C
+import qualified Data.ByteString.Char8 as C
+
+-- Type synonyms for fields in a fastq record
+type Name = C.ByteString
+type Nucleotides = C.ByteString
+type Qualities = C.ByteString
+
+-- New type for a fastq record
+data Fastq = Fastq Name Nucleotides Qualities
+
+-- Turn a fastq record into text.
+formatFastq :: Fastq -> C.ByteString
+formatFastq (Fastq n s q) =
+    C.unlines [n, s, "+", q]
+
+{-
+Parse lines four by four, ignoring the third with "_".
+We use pattern-matching and recursion to achieve this.
+-}
+getFastqs :: [C.ByteString] -> [Fastq]
+getFastqs [] = []
+getFastqs (l1 : l2 : _ : l4 : ls) =
+    Fastq l1 l2 l4 : getFastqs ls
+
+
+trimTtails :: [Fastq] -> [Fastq]
+trimTtails [] = []
+trimTtails (Fastq n s q : fs) =
+    let (s', q') = zipTrim s q
+    in Fastq n s' q' : trimTtails fs
+
+
+zipTrim :: Nucleotides -> Qualities -> (Nucleotides, Qualities)
+{-
+We don't check that the qualities have the same length
+as the sequences, but they should.
+-}
+zipTrim s q
+    | C.null s = (C.empty, C.empty)
+    | C.head (last $ C.group s) == 'T' =
+        C.unzip (C.zip (C.concat $ init $ C.group s) q)
+    | otherwise = (s, q)
+
+
+-- Compose functions into a "pipeline".
+processLines :: [C.ByteString] -> [C.ByteString]
+processLines =
+    map formatFastq . trimTtails . getFastqs
+
+{-
+C.lines decomposes the text into lines which are
+processed by processLines to remove duplicates.
+C.concat "flattens" the resulting list of
+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.
+-}
+main :: IO ()
+main = C.interact (C.concat . processLines . C.lines)

trim-t-tail-from-fastq/Haskell/stack.yaml

+# This file was automatically generated by 'stack init'
+#
+# Some commonly used options have been documented as comments in this file.
+# For advanced use and comprehensive documentation of the format, please see:
+# http://docs.haskellstack.org/en/stable/yaml_configuration/
+
+# Resolver to choose a 'specific' stackage snapshot or a compiler version.
+# A snapshot resolver dictates the compiler version and the set of packages
+# to be used for project dependencies. For example:
+#
+# resolver: lts-3.5
+# resolver: nightly-2015-09-21
+# resolver: ghc-7.10.2
+# resolver: ghcjs-0.1.0_ghc-7.10.2
+# resolver:
+#  name: custom-snapshot
+#  location: "./custom-snapshot.yaml"
+resolver: lts-7.1
+
+# User packages to be built.
+# Various formats can be used as shown in the example below.
+#
+# packages:
+# - some-directory
+# - https://example.com/foo/bar/baz-0.0.2.tar.gz
+# - location:
+#    git: https://github.com/commercialhaskell/stack.git
+#    commit: e7b331f14bcffb8367cd58fbfc8b40ec7642100a
+# - location: https://github.com/commercialhaskell/stack/commit/e7b331f14bcffb8367cd58fbfc8b40ec7642100a
+#   extra-dep: true
+#  subdirs:
+#  - auto-update
+#  - wai
+#
+# A package marked 'extra-dep: true' will only be built if demanded by a
+# non-dependency (i.e. a user package), and its test suites and benchmarks
+# will not be run. This is useful for tweaking upstream packages.
+packages:
+- '.'
+# Dependency packages to be pulled from upstream that are not in the resolver
+# (e.g., acme-missiles-0.3)
+extra-deps: []
+
+# Override default flag values for local packages and extra-deps
+flags: {}
+
+# Extra package databases containing global packages
+extra-package-dbs: []
+
+# Control whether we use the GHC we find on the path
+# system-ghc: true
+#
+# Require a specific version of stack, using version ranges
+# require-stack-version: -any # Default
+# require-stack-version: ">=1.2"
+#
+# Override the architecture used by stack, especially useful on Windows
+# arch: i386
+# arch: x86_64
+#
+# Extra directories used by stack for building
+# extra-include-dirs: [/path/to/dir]
+# extra-lib-dirs: [/path/to/dir]
+#
+# Allow a newer minor version of GHC than the snapshot specifies
+# compiler-check: newer-minor
+ghc-options:
+    "*": -O -Wall
+rebuild-ghc-options:
+    true

trim-t-tail-from-fastq/Haskell/trim-t-tail-from-fastq.cabal

+name:                trim-t-tail-from-fastq
+version:             0.1.0.0
+synopsis:            Simple project template from stack
+description:         Please see README.md
+homepage:            https://github.com/blaiseli/trim-t-tail-from-fastq#readme
+license:             BSD3
+license-file:        LICENSE
+author:              Blaise Li
+maintainer:          blaise.li@normalesup.org
+copyright:           (CC-BY-SA) Blaise Li
+category:            Bioinformatics
+build-type:          Simple
+cabal-version:       >=1.10
+
+executable trim-t-tail-from-fastq
+  hs-source-dirs:      src
+  main-is:             Main.hs
+  default-language:    Haskell2010
+  build-depends:       base >= 4.7 && < 5, bytestring