src/hg/hgTrackUi/hgTrackUi.c 1.513
1.513 2010/01/12 23:36:03 angie
In bamUi, add baseColor defaults to tdb if this is a custom track, as we do in hgTracks.c. Otherwise baseColor drop-down doesn't appear for BAM custom tracks.
Index: src/hg/hgTrackUi/hgTrackUi.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTrackUi/hgTrackUi.c,v
retrieving revision 1.512
retrieving revision 1.513
diff -b -B -U 4 -r1.512 -r1.513
--- src/hg/hgTrackUi/hgTrackUi.c 8 Jan 2010 18:11:02 -0000 1.512
+++ src/hg/hgTrackUi/hgTrackUi.c 12 Jan 2010 23:36:03 -0000 1.513
@@ -2174,9 +2174,9 @@
} \
} \
}\""
-void bamUi(struct trackDb *tdb)
+void bamUi(struct trackDb *tdb, struct customTrack *ct)
/* BAM: short-read-oriented alignment file format. */
{
char cartVarName[1024];
boolean canPair = (trackDbSetting(tdb, BAM_PAIR_ENDS_BY_NAME) != NULL);
@@ -2192,8 +2192,16 @@
safef(cartVarName, sizeof(cartVarName), "%s." BAM_MIN_ALI_QUAL, tdb->tableName);
cartMakeIntVar(cart, cartVarName,
atoi(trackDbSettingOrDefault(tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT)), 4);
puts("<BR>");
+if (ct)
+ {
+ // Auto-magic baseColor defaults for BAM, same as in hgTracks.c newCustomTrack
+ hashAdd(tdb->settingsHash, BASE_COLOR_USE_SEQUENCE, cloneString("lfExtra"));
+ hashAdd(tdb->settingsHash, BASE_COLOR_DEFAULT, cloneString("diffBases"));
+ hashAdd(tdb->settingsHash, SHOW_DIFF_BASES_ALL_SCALES, cloneString("."));
+ hashAdd(tdb->settingsHash, "showDiffBasesMaxZoom", cloneString("100"));
+ }
baseColorDrawOptDropDown(cart, tdb);
printf("<BR>\n");
printf("<B>Additional coloring modes:</B><BR>\n");
safef(cartVarName, sizeof(cartVarName), "%s." BAM_COLOR_MODE, tdb->tableName);
@@ -2426,9 +2434,9 @@
else if (sameString(track, "dgv") || (startsWith("dgvV", track) && isdigit(track[4])))
dgvUi(tdb);
#ifdef USE_BAM
else if (sameString(tdb->type, "bam"))
- bamUi(tdb);
+ bamUi(tdb, ct);
#endif
else if (tdb->type != NULL)
{
/* handle all tracks with type genePred or bed or "psl xeno <otherDb>" */