fixed issue where file reader stalls at the pre-handled fasta header

steineggerlab · Oct 19, 2022 · b839579 · b839579
1 parent a86fed8
commit b839579
Showing 1 changed file with 8 additions and 1 deletion.
diff --git a/src/process/ContigDragProcess.java b/src/process/ContigDragProcess.java
@@ -38,7 +38,7 @@ public static List<String> drag(String seqPath, BlockProfileEntity bp) throws ja
 
 					FileStream outStream = new FileStream(ctgPath, 'w');
 					outStream.isTemp();
-					Prompt.talk("Dragging block-containing contig " + bp.getCtg(ci) +
+					Prompt.talk("Dragging block-containing contig " + ctg +
 							" from the assembly on : " + ANSIHandler.wrapper(outStream.PATH, 'y'));
 
 					outStream.println(line);				
@@ -51,6 +51,13 @@ public static List<String> drag(String seqPath, BlockProfileEntity bp) throws ja
 
 					outStream.close();	
 				}
+				else {
+					line = seqStream.readLine();
+					while(line != null) {
+						if(line.startsWith(">")) break;
+						line = seqStream.readLine();
+					}
+				}
 				ci++;
 			}
 			else {