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/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
index 183e284..72c1117 100755
--- src/userApps/fetchKentSource.sh
+++ src/userApps/fetchKentSource.sh
@@ -2,40 +2,30 @@
 #
 # exit on any error:
 set -beEu -o pipefail
 
 # switching to beta for version 286
 export branch="beta"
 
 # to use the top of the source tree, uncomment this branch=HEAD statment
 # and comment out the one above.  This is sometimes useful when there
 # are new fixes in the source tree in between beta releases.
 # Note, the top of the source tree could be broken at any time, it is on
 # a 10-minute update cycle with live work taking place.
 
 # export branch="HEAD"
 
-# script to fetch extra source to use with the kent build,
-# and then selectively parts of the kent source tree, enough to
-# build just the user utilities
-
-# the combined samtabix source for the SAM/BAM/TABIX functions:
-rm -fr samtabix
-echo "fetch samtabix" 1>&2
-git clone http://genome-source.cse.ucsc.edu/samtabix.git samtabix \
-  > /dev/null 2>&1
-
 # These selective git archive commands only work up to a certain size
 # of fetched source (number of arguments), hence the multiple set of
 # individual fetches to get all the parts
 
 rm -f part1Src.zip part2Src.zip part3Src.zip part4Src.zip part5Src.zip
 export partNumber=1
 export ofN="of 5"
 
 # this util changed from being in a directory to being a script
 # the extract can't overwrite the directory with a file
 rm -fr kent/src/utils/uniprotLift
 
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
@@ -283,26 +273,27 @@
 src/hg/makeDb/hgWaba \
 src/hg/makeDb/ldHgGene \
 src/hg/makeDb/hgMrnaRefseq \
 src/hg/makeDb/schema \
 src/hg/makeDb/tfbsConsLoc \
 src/hg/makeDb/tfbsConsSort > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip
 
 ((partNumber++))
 echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
 
 git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
 --prefix=kent/ ${branch} \
 src/parasol \
+src/htslib \
 src/hg/pslToChain \
 src/hg/makeDb/outside \
 src/hg/makeDb/trackDbRaFormat \
 src/hg/makeDb/trackDbPatch \
 src/hg/mouseStuff \
 src/hg/ratStuff \
 src/hg/nci60 \
 src/hg/visiGene/knownToVisiGene \
 src/hg/visiGene/hgVisiGene > part${partNumber}Src.zip
 
 unzip -o -q part${partNumber}Src.zip