smarter bash completion

Author: lomereiter

etc/bash_completion.d/sambamba

@@ -51,9 +51,21 @@ _sambamba()
     elif [[ ${COMP_WORDS[COMP_CWORD - 2]} == "--format" || ${COMP_WORDS[COMP_CWORD - 1]} == "-f" ]]; then
         COMPREPLY=( $(compgen -W "sam bam json msgpack" -- $cur) )
         compopt +o nospace
+    elif [[ $subcommand == "view" || $subcommand == "slice" ]]; then
+        for word in ${COMP_WORDS[@]}; do
+            if [[ $word == *.bam && $word != "" ]]; then
+                eval abspath=$word
+                COMPREPLY=( $(sambamba view -H $abspath | grep @SQ | \
+                              cut -f 2 | cut -f2 -d: 2>/dev/null | grep "^$cur") )
+                break
+            fi
+        done
+        compopt -o default
+        compopt -o filenames
     else
         compopt -o default
     fi
 }
 
 complete -o nospace -F _sambamba sambamba
+# vim: set syntax=sh :