0b52ad3ec2c6113bfdd692a58fee812b7dd0a7b2
kent
  Fri Feb 4 20:47:27 2011 -0800
Getting Table Browser to handle BAM files.  This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
diff --git src/hg/hgTables/makefile src/hg/hgTables/makefile
index b20607e..8142e3d 100644
--- src/hg/hgTables/makefile
+++ src/hg/hgTables/makefile
@@ -1,26 +1,27 @@
 include ../../inc/common.mk
 
 L += -lm ${MYSQLLIBS}
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 A = hgTables
 
 T = tstbug.o
 
-O = $A.o asObj.o bam.o bedList.o bigBed.o bigWig.o chromGraph.o compositeTrack.o custom.o filterFields.o \
+O = $A.o asFilter.o asObj.o bam.o bedList.o bigBed.o bigWig.o \
+    chromGraph.o compositeTrack.o custom.o filterFields.o \
     gffOut.o identifiers.o intersect.o correlate.o correlatePlot.o \
     joining.o maf.o mainPage.o microarrayTables.o rangeHistogram.o schema.o pal.o \
     seqOut.o sumStats.o usage.o wiggle.o wikiTrack.o galaxy.o great.o userRegions.o
 
 include ../../inc/cgi_build_rules.mk
 
 rsyncDataOpts = --times --recursive --executability --omit-dir-times --cvs-exclude --delete
 
 my::
 	rm -f ${CGI_BIN}-${USER}/all.joiner
 	cp ../makeDb/schema/all.joiner ${CGI_BIN}-${USER}
 	rm -rf ${CGI_BIN}-${USER}/greatData
 	rsync ${rsyncDataOpts} greatData ${CGI_BIN}-${USER}/
 	chmod -R a+rX ${CGI_BIN}-${USER}/greatData
 	chmod a+r ${CGI_BIN}-${USER}/all.joiner