#141 sort with multiple thread support to improve performance

[wangyugui]

sort command is used in terminator, but it need multiple thread support to improve performance.

sort command is used by 'XXXX|sort -k2.5,2 -k4,4n -k5,5n' in terminator.

'sort -k2.5,2 -k4,4n -k5,5n ref.fa >x.fa' will have the default max 8 thread support.
'sort --parallel=32 -k2.5,2 -k4,4n -k5,5n ref.fa >x.fa' will have the default 32 thread support.

but when used a pipe input, there will be no mutiple thread support in sort event with --parallel=32.
cat ref.fa |sort -k2.5,2 -k4,4n -k5,5n >x.fa ==>single thread
cat ref.fa |sort --parallel=32 -k2.5,2 -k4,4n -k5,5n >x.fa ==>single thread

it will need a lit fix only, but I can't fix perl source.

[wangyugui]

and the sort in terminator will use 1279m or more time, so we need to improve the performance of it.

[wangyugui]

my friend give a dirty fix. i will test it.

```
Index: bin/caqc.pl
--- bin/caqc.pl (revision 676)
+++ bin/caqc.pl (working copy)
@@ -1751,8 +1751,9 @@

 # sort on UID of UTG, or CCO, then begin position, then end
 # UTGs should only be unplaced surrogates

- open( BADMATES, "	sort -k2.5,2 -k4,4n -k5,5n > $badMateFile" )
+ #open( BADMATES, "	sort -k2.5,2 -k4,4n -k5,5n > $badMateFile" )
+ #		die "Couldn't write to $badMateFile.";
+ open( BADMATES, ">","$badMateFile.tmp" );
local $\ = "\n";
local $, = "\t";
while ( my ( $badId, $coord ) = each %bad_mates ) {
@@ -1764,6 +1765,8 @@
}
}
close BADMATES;
+
+ system("sort --parallel=32 -k2.5,2 -k4,4n -k5,5n $badMateFile.tmp > $badMateFile");

 exit(0);

}
```

[wangyugui]

the dirty fix seems work. please close this ticket.