11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index fd7259b..a2e73d3 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -4204,34 +4204,32 @@
 	}
     //add bedDetail here
     else if (startsWith("bedDetail", type))
         {
         doBedDetail(tdb, NULL, item);
         }
     else if (sameString(type, "interaction") )
 	{
 	int num = 12;
         genericBedClick(conn, tdb, item, start, num);
 	}
     else if (startsWith("gvf", type))
         {
         doGvf(tdb, item);
         }
-#ifdef USE_BAM
     else if (sameString(type, "bam"))
 	doBamDetails(tdb, item);
-#endif // USE_BAM
     else if ( startsWith("longTabix", type))
 	doLongTabix(tdb, item);
     }
 if (imagePath)
     {
     char *bigImagePath = trackDbSettingClosestToHome(tdb, ITEM_BIG_IMAGE_PATH);
     char *bothWords[2];
     int shouldBeTwo = chopLine(imagePath, bothWords);
     if (shouldBeTwo != 2)
 	errAbort("itemImagePath setting for %s track incorrect. Needs to be \"itemImagePath <path> <suffix>\".", tdb->track);
     printf("<BR><IMG SRC=\"%s/%s.%s\"><BR><BR>\n", bothWords[0], item, bothWords[1]);
     shouldBeTwo = chopLine(bigImagePath, bothWords);
     if (shouldBeTwo != 2)
 	errAbort("bigItemImagePath setting for %s track incorrect. Needs to be \"itemImagePath <path> <suffix>\".", tdb->track);
     printf("<A HREF=\"%s/%s.%s\">Download Original Image</A><BR>\n", bothWords[0], item, bothWords[1]);
@@ -20846,38 +20844,34 @@
     doExpRatio(ct->tdb, fileItem, ct);
 else if ( startsWith( "longTabix", type))
     doLongTabix(ct->tdb, item);
 else if (sameWord(type, "encodePeak"))
     doEncodePeak(ct->tdb, ct, fileName);
 else if (sameWord(type, "bigWig"))
     bigWigCustomClick(ct->tdb);
 else if (sameWord(type, "bigChain"))
     genericChainClick(NULL, ct->tdb, item, start, "seq");
 else if (sameWord(type, "bigPsl"))
     genericBigPslClick(NULL, ct->tdb, item, start, end);
 else if (sameWord(type, "bigMaf"))
     genericMafClick(NULL, ct->tdb, item, start);
 else if (sameWord(type, "bigBed") || sameWord(type, "bigGenePred"))
     bigBedCustomClick(ct->tdb);
-#ifdef USE_BAM
 else if (sameWord(type, "bam"))
     doBamDetails(ct->tdb, itemName);
-#endif//def USE_BAM
-#ifdef USE_TABIX
 else if (sameWord(type, "vcfTabix"))
     doVcfTabixDetails(ct->tdb, itemName);
-#endif//def USE_TABIX
 else if (sameWord(type, "vcf"))
     doVcfDetails(ct->tdb, itemName);
 else if (sameWord(type, "makeItems"))
     doMakeItemsDetails(ct, fileName);	// fileName is first word, which is, go figure, id
 else if (ct->wiggle)
     {
     if (ct->dbTrack)
 	{
 	struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
 	genericWiggleClick(conn, ct->tdb, fileItem, start);
 	hFreeConn(&conn);
 	}
     else
 	genericWiggleClick(NULL, ct->tdb, fileItem, start);
     /*	the NULL is for conn, don't need that for custom tracks */
@@ -26141,36 +26135,34 @@
     {
     htcLrgCdna(item);
     }
 else if (startsWith("peptideAtlas", table))
     {
     doPeptideAtlas(tdb, item);
     }
 else if (startsWith("gtexGene", table))
     {
     doGtexGeneExpr(tdb, item);
     }
 else if (startsWith("snake", trackHubSkipHubName(table)))
     {
     doSnakeClick(tdb, item);
     }
-#ifdef USE_TABIX
 else if (tdb != NULL && startsWithWord("vcfTabix", tdb->type))
     {
     doVcfTabixDetails(tdb, item);
     }
-#endif // USE_TABIX
 else if (tdb != NULL && startsWithWord("vcf", tdb->type))
     {
     doVcfDetails(tdb, item);
     }
 else if (tdb != NULL)
     {
     genericClickHandler(tdb, item, NULL);
     }
 else
     {
     cartWebStart(cart, database, "%s", track);
     printf("Sorry, clicking there doesn't do anything yet (%s).", track);
     }
 /* End of 1000+ line dispatch on table involving 100+ if/elses. */