From a50944913c975d7d6f088f51962c6e9e484cc43c Mon Sep 17 00:00:00 2001
From: Damien Zammit <damien@zamaudio.com>
Date: Mon, 18 Sep 2023 18:34:23 +1000
Subject: Fix whitespace

---
 ruffsort.cpp | 43 +++++++++++++++++++++++--------------------
 1 file changed, 23 insertions(+), 20 deletions(-)

diff --git a/ruffsort.cpp b/ruffsort.cpp
index d1b4189..4b43659 100644
--- a/ruffsort.cpp
+++ b/ruffsort.cpp
@@ -96,34 +96,36 @@ main(int argc, char* argv[]) {
         break;
       case 'r':
         refseq = string(optarg);
-	refseqsa = refseq + string(".sa");
+        refseqsa = refseq + string(".sa");
         is.open (refseqsa.c_str(), ios::in);
-	if (!is.good()) {
-	  cerr << "reference has no suffix array generated, indexing now" << endl;
+        if (!is.good()) {
+          cerr << "reference has no suffix array generated, indexing now" << endl;
           is.open (refseq.c_str(), ios::in);
           if (!is.good()) {
             cerr << "cannot open input file " << optarg << endl;
             exit (-1);
           }
-	  fastastring seqs;
-	  is >> seqs;
-	  seqs.push_back('~');
-	  sa_fasta tree(seqs);
-	  is.close();
-	  tree.savesarray(refseqsa);
+          fastastring seqs;
+          is >> seqs;
+          seqs.push_back('~');
+          sa_fasta tree(seqs);
+          is.close();
+          tree.savesarray(refseqsa);
           cout << "Suffix array generated" << endl;
-	}
-	is.close();
-	break;
+        }
+        is.close();
+        break;
       case 'q':
         iq.open (optarg, ios::in);
-	if (!iq.good()) {
-	  cerr << "query fastq missing" << endl;
-	  exit (-1);
-	}
-	break;
+        if (!iq.good()) {
+          cerr << "query fastq missing" << endl;
+          usage();
+          exit (-1);
+        }
+        break;
       default:
         cerr << "unknown argument " << opt << endl;
+        usage();
         exit (-1);
         break;
     }
@@ -132,6 +134,7 @@ main(int argc, char* argv[]) {
   is.open (refseq.c_str(), ios::in);
   if (!is.good()) {
     cerr << "cannot open ref file" << endl;
+    usage();
     exit (-1);
   }
   
@@ -147,10 +150,10 @@ main(int argc, char* argv[]) {
   fastastring totest;
   iq >> totest;
   try {
-  	result = tree.find_position(totest, 'N');
+    result = tree.find_position(totest, 'N');
   } catch (StringNotFound) {
-  	cerr << "Not found" << endl;
-	exit (0);
+    cerr << "Not found" << endl;
+    exit (0);
   }
   cout << result << endl;
 }
-- 
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