312002c4b4015a4e5acedd47dad9e5d6b8d3c1b1
markd
  Mon Nov 22 18:38:59 2021 -0800
move rmskAlign and rmskJoined to lib so it they can be used by programs

diff --git src/hg/lib/makefile src/hg/lib/makefile
index 0c3059f..ce4c202 100644
--- src/hg/lib/makefile
+++ src/hg/lib/makefile
@@ -18,31 +18,31 @@
   encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodePdb.o \
   encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeTag.o \
   encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o \
   encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode3/encode3Valid.o \
   estOrientInfo.o expData.o expRecord.o facetField.o facetedTable.o featureBits.o findKGAlias.o \
   findKGProtAlias.o gcPercent.o genark.o genbank.o genbankBlackList.o gencodeAttrs.o gencodeToRefSeq.o geneGraph.o \
   genePred.o genePredReader.o geoMirror.o ggCluster.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o \
   googleAnalytics.o gpFx.o grp.o gtexAse.o gtexDonor.o gtexGeneBed.o gtexInfo.o gtexSample.o \
   gtexSampleData.o gtexTissue.o gtexTissueMedian.o gtexUi.o hCommon.o hPrint.o hVarSubst.o \
   hapmapAllelesOrtho.o hapmapPhaseIIISummary.o hapmapSnps.o hdb.o hgColors.o hgConfig.o hgFind.o \
   hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgMaf.o hgRelate.o hic.o hicUi.o hubConnect.o hubPublic.o \
   hubSearchText.o hui.o imageClone.o indelShift.o interact.o interactUi.o itemAttr.o jksql.o joiner.o \
   jsHelper.o kgAlias.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o lav.o lfs.o liftOver.o liftOverChain.o \
   liftUp.o longRange.o lrg.o lsSnpPdb.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mdb.o \
   microarray.o minChromSize.o netAlign.o netCart.o pepPred.o pgPhenoAssoc.o pgSnp.o pslReader.o qaSeq.o \
-  rankProp.o refLink.o rikenCluster.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o \
+  rankProp.o refLink.o rikenCluster.o rmskAlign.o rmskJoined.o rmskOut.o rmskOut2.o rnaGene.o sage.o sageCounts.o samAlignment.o \
   sample.o sanger22extra.o scoredRef.o seqWindow.o snakeUi.o snp.o snpExceptions.o soTerm.o spDb.o sqlProg.o \
   sqlSanity.o stanMad.o stsAlias.o stsInfo2.o stsMap.o stsMarker.o tableStatus.o tablesTables.o \
   tagRepo.o tfbsCons.o tigrCmrGene.o traceInfo.o trackDb.o trackDbCache.o trackDbCustom.o trackHub.o \
   trackVersion.o trashDir.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txGraph.o txInfo.o txRnaAccs.o \
   variantProjector.o vcfUi.o vegaInfo.o web.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o \
   wiggleUtils.o wikiLink.o
 
 ifeq (${USE_HIC}, 1)
   O += straw.o
 endif
 
 ifeq (${GBROWSE}, 1)
   GBROWSE_D=-DGBROWSE
 else
   GBROWSE_D=