From 579176dd1e7dc465a2a0c1655cb687dc55bd1e45 Mon Sep 17 00:00:00 2001
From: mikessh <mikhail.shugay@gmail.com>
Date: Wed, 15 Feb 2017 17:17:23 +0300
Subject: [PATCH] #62: 2prev

---
 .../vdjtools/io/parser/ClonotypeStreamParser.groovy         | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/main/groovy/com/antigenomics/vdjtools/io/parser/ClonotypeStreamParser.groovy b/src/main/groovy/com/antigenomics/vdjtools/io/parser/ClonotypeStreamParser.groovy
index f96c2d8e..088be2f4 100644
--- a/src/main/groovy/com/antigenomics/vdjtools/io/parser/ClonotypeStreamParser.groovy
+++ b/src/main/groovy/com/antigenomics/vdjtools/io/parser/ClonotypeStreamParser.groovy
@@ -149,6 +149,10 @@ public abstract class ClonotypeStreamParser implements Iterable<Clonotype> {
                 return null
             }
 
+            if (clonotypeString.trim().empty) {
+                return null // ignore blank lines
+            }
+
             totalLines++
 
             def clonotype = innerParse(clonotypeString)
@@ -182,7 +186,7 @@ public abstract class ClonotypeStreamParser implements Iterable<Clonotype> {
             return clonotype
         } catch (Exception e) {
             throw new RuntimeException("Unable to parse clonotype string $clonotypeString " +
-                    "for $software input type.", e)
+                    "for $software input type: ${e.message}", e)
         }
     }