src/hg/hgTracks/bamTrack.c 1.22

1.22 2010/01/05 00:34:49 angie
pairSearchRange can yield many items that are completely out of the window. Exclude those from tg->items so they don't inflate the item count and scare us off of making map links.

Index: src/hg/hgTracks/bamTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bamTrack.c,v
retrieving revision 1.21
retrieving revision 1.22
diff -b -B -U 4 -r1.21 -r1.22
--- src/hg/hgTracks/bamTrack.c	21 Dec 2009 22:43:32 -0000	1.21
+++ src/hg/hgTracks/bamTrack.c	5 Jan 2010 00:34:49 -0000	1.22
@@ -256,8 +256,9 @@
 struct linkedFeatures *lf = bamToLf(bam, data);
 struct track *tg = btd->tg;
 if (!(core->flag & BAM_FPAIRED) || (core->flag & BAM_FMUNMAP))
     {
+    if (lf->start < winEnd && lf->end > winStart)
     slAddHead(&(tg->items), lfsFromLf(lf));
     }
 else
     {
@@ -295,8 +296,9 @@
 	}
     else
 	{
 	lfMate->next = lf;
+	if (min(lfMate->start, lf->start) < winEnd && max(lfMate->end, lf->end) > winStart)
 	slAddHead(&(tg->items), lfsFromLf(lfMate));
 	hashRemove(btd->pairHash, lf->name);
 	}
     }