src/lib/blastParse.c 1.25

Index: src/lib/blastParse.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/blastParse.c,v
retrieving revision 1.24
retrieving revision 1.25
diff -b -B -U 4 -r1.24 -r1.25
--- src/lib/blastParse.c	12 Apr 2009 18:45:54 -0000	1.24
+++ src/lib/blastParse.c	6 Jan 2010 21:09:18 -0000	1.25
@@ -631,8 +631,12 @@
  *   Identities = 256/400 (64%), Positives = 306/400 (76%)
  *   Frame = +1 / -2
  *     (tblastn)
  *
+ *   Identities = 1317/10108 (13%), Positives = 2779/10108 (27%), Gaps = 1040/10108
+ *   (10%)
+ *      - wrap on long lines
+ *
  * Handle weird cases where the is only a `Score' line, with no `Identities'
  * lines by skipping the alignment; they seem line small, junky alignments.
  */
 line = bfNeedNextLine(bf);
@@ -665,16 +669,20 @@
     bb->tStrand = words[10][0];
     bb->tFrame = atoi(words[10]);
     }
 
+line = bfNeedNextLine(bf);
+boolean wrapped = (startsWith("(", line));
+
 /* Process something like:
  *     Strand = Plus / Plus (blastn)
  *     Frame = +1           (tblastn)
  *     Frame = +1 / -2      (tblastx)
  *     <blank line>         (blastp)
  * note that wu-tblastn puts frame on Identities line
  */
-line = bfNeedNextLine(bf);
+if (wrapped)
+    line = bfNeedNextLine(bf);
 wordCount = chopLine(line, words);
 if ((wordCount >= 5) && sameWord("Strand", words[0]))
     {
     bb->qStrand = getStrand(bf, words[2]);