close #231

Makefile.am

@@ -90,3 +90,10 @@ clean-local-check:
 utilities: utilities/dataExplore.r utilities/interpretDEploid.r
 	sed -i'.bak' -e '/#!\/usr\/bin\/env Rscript/d' -e '/rm(list=ls())/d' utilities/dataExplore.r ; echo "#!/usr/bin/env Rscript" > tmpTxt; echo "rm(list=ls()); dEploidRootDir=\"$(PWD)\"" >> tmpTxt ; cat utilities/dataExplore.r >> tmpTxt ; mv tmpTxt utilities/dataExplore.r; chmod a+x utilities/dataExplore.r;
 	sed -i'.bak' -e '/#!\/usr\/bin\/env Rscript/d' -e '/rm(list=ls())/d' utilities/interpretDEploid.r; echo "#!/usr/bin/env Rscript" > tmpTxt; echo "rm(list=ls()); dEploidRootDir=\"$(PWD)\"" >> tmpTxt ; cat utilities/interpretDEploid.r >> tmpTxt ; mv tmpTxt utilities/interpretDEploid.r; chmod a+x utilities/interpretDEploid.r
+
+
+if ENABLE_BASH_COMPLETION
+bashcompletiondir = $(BASH_COMPLETION_DIR)
+dist_bashcompletion_DATA = dEploid_completion.sh
+endif
+

configure.ac

@@ -42,6 +42,25 @@ AC_TYPE_SIZE_T
   #AC_SUBST(OPT_CXXFLAGS)
 #fi
 
+# bash complete
+AC_ARG_WITH([bash-completion-dir],
+    AS_HELP_STRING([--with-bash-completion-dir[=PATH]],
+        [Install the bash auto-completion script in this directory. @<:@default=yes@:>@]),
+    [],
+    [with_bash_completion_dir=yes])
+
+if test "x$with_bash_completion_dir" = "xyes"; then
+    PKG_CHECK_MODULES([BASH_COMPLETION], [bash-completion >= 2.0],
+        [BASH_COMPLETION_DIR="`pkg-config --variable=completionsdir bash-completion`"],
+        [BASH_COMPLETION_DIR="$datadir/bash-completion/completions"])
+else
+    BASH_COMPLETION_DIR="$with_bash_completion_dir"
+fi
+
+AC_SUBST([BASH_COMPLETION_DIR])
+AM_CONDITIONAL([ENABLE_BASH_COMPLETION],[test "x$with_bash_completion_dir" != "xno"])
+
+
 # Enable Warnings
 AX_CXXFLAGS_WARN_ALL
 #AX_CHECK_COMPILE_FLAG([-Wextra], [OPT_CXXFLAGS="$OPT_CXXFLAGS -Wextra"], [], [-Werror])

dEploid_completion.sh

@@ -0,0 +1,41 @@
+#/usr/bin/env bash
+
+_dEploid_completions()
+{
+    local cur prev opts
+    COMPREPLY=()
+    cur="${COMP_WORDS[COMP_CWORD]}"
+    prev="${COMP_WORDS[COMP_CWORD-1]}"
+    opts="-h -help \
+    -ref -alt -plaf -panel -exclude\
+    -vcf -sample -plafFromVcf \
+    -o -seed -noPanel\
+    -ibd -lasso -best"
+
+
+    if [[ ${cur} == -* || ${prev} == "dEploid" ]] ; then
+        COMPREPLY=( $(compgen -W "${opts}" -- ${cur}) )
+        return 0
+    else
+        if [[ ${prev} == "-ref" || ${prev} == "-alt" || ${prev} == "-plaf" || ${prev} == "-panel" || ${prev} == "-exclude" ]] ; then
+            COMPREPLY=( $(compgen -o plusdirs -f -X '!*.@(txt|gz)' -- ${cur}) )
+            for ((i=0; i < ${#COMPREPLY[@]}; i++)); do
+                [ -d "${COMPREPLY[$i]}" ] && COMPREPLY[$i]=${COMPREPLY[$i]}/
+            done
+            return 0
+        else
+            if [[ ${prev} == "-vcf" ]] ; then
+                COMPREPLY=( $(compgen -o plusdirs -f -X '!*.@(vcf|gz)' -- ${cur}) )
+                for ((i=0; i < ${#COMPREPLY[@]}; i++)); do
+                    [ -d "${COMPREPLY[$i]}" ] && COMPREPLY[$i]=${COMPREPLY[$i]}/
+                done
+                return 0
+            else
+                return 0
+            fi
+        fi
+    fi
+    return 0
+}
+
+complete -o filenames -o nospace -o bashdefault -F _dEploid_completions dEploid