1e01f41fc6811a3ba9efc853e01a94839f7a91fb
braney
  Thu Mar 31 09:42:58 2011 -0700
add compare routine for cBlocks based on query position
diff --git src/inc/chain.h src/inc/chain.h
index b7bd9c7..6be0f2a 100644
--- src/inc/chain.h
+++ src/inc/chain.h
@@ -12,30 +12,33 @@
 
 #ifndef BITS_H
 #include "bits.h"
 #endif
 
 struct cBlock
 /* A gapless part of a chain. */
     {
     struct cBlock *next;	/* Next in list. */
     int tStart,tEnd;		/* Range covered in target. */
     int qStart,qEnd;		/* Range covered in query. */
     int score;	 	 	/* Score of block. */
     void *data;			/* Some associated data pointer. */
     };
 
+int cBlockCmpQuery(const void *va, const void *vb);
+/* Compare to sort based on query start. */
+
 int cBlockCmpTarget(const void *va, const void *vb);
 /* Compare to sort based on target start. */
 
 int cBlockCmpBoth(const void *va, const void *vb);
 /* Compare to sort based on query, then target. */
 
 int cBlockCmpDiagQuery(const void *va, const void *vb);
 /* Compare to sort based on diagonal, then query. */
 
 void cBlocksAddOffset(struct cBlock *blockList, int qOff, int tOff);
 /* Add offsets to block list. */
 
 struct cBlock *cBlocksFromAliSym(int symCount, char *qSym, char *tSym, 
         int qPos, int tPos);
 /* Convert alignment from alignment symbol (bases and dashes) format