src/hg/snp/snpLoad/makefile 1.47

Index: src/hg/snp/snpLoad/makefile
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/snp/snpLoad/makefile,v
retrieving revision 1.46
retrieving revision 1.47
diff -b -B -U 1000000 -r1.46 -r1.47
--- src/hg/snp/snpLoad/makefile	6 Mar 2009 23:37:57 -0000	1.46
+++ src/hg/snp/snpLoad/makefile	10 Mar 2009 00:34:34 -0000	1.47
@@ -1,220 +1,220 @@
 include ../../../inc/common.mk
 
-L = ${MYSQLLIBS} -lm
+L += ${MYSQLLIBS} -lm
 MYLIBDIR = ../../../lib/${MACHTYPE}
 MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a
 
 all: snpNcbiToUcsc hapmapPhaseIIISummary
 
 S = snpNcbiToUcsc
 ${S}: ${S}.o ${MYLIBS}
 	${CC} ${COPT} -o ${BINDIR}/${S} ${S}.o ${MYLIBS} $L
 	${STRIP} ${BINDIR}/${S}${EXE}
 
 H = hapmapPhaseIIISummary
 ${H}: ${H}.o ${MYLIBS}
 	${CC} ${COPT} -o ${BINDIR}/${H} ${H}.o ${MYLIBS} $L
 	${STRIP} ${BINDIR}/${H}${EXE}
 
 O = affyLookup.o cnpLookup.o fetchSeq.o \
     hapmap1.o hapmap2.o hapmapLookup.o hapmapMixed.o \
     hapmapOrtho.o hapmapSummary.o hapmapValidate.o \
     illuminaLookup.o \
     illuminaLookup2.o \
     illuminaLookup1M.o \
     snpCheckAlleles.o snpCheckClassAndObserved.o snpCheckCluster.o snpCheckCluster2.o \
     snpClassAndObserved.o snpCleanSeq.o snpCompareLoctype.o snpCompareWeight.o \
     snpContigLocFilter.o snpContigLocFilter125.o \
     snpContigLocusIdCondense.o snpContigLocusIdFilter.o snpContigLocusIdFilter125.o \
     snpExpandAllele.o snpFinalTable.o snpFreq.o snpFunction.o \
     snpGetDeletions.o snpGetInsertions.o snpGetSeqDup.o snpGetSimple.o \
     snpLoadFasta.o snpLocType.o snpLocType125.o \
     snpMissing.o snpMoltype.o snpMultiple.o \
     snpOrtho.o snpOrthoJoin.o \
     snpOrthoLookup.o snpPAR.o \
     snpReadFasta.o snpReadSeq.o snpReadSeq2.o snpRefUCSC.o \
     snpSort.o snpSplitByChrom.o snpSplitByChrom2.o snpSNP.o \
     subSnpCondense.o trimHeader.o
 
 old: affyLookup cnpLookup fetchSeq \
      hapmap1 hapmap2 hapmapLookup hapmapMixed \
      hapmapOrtho hapmapSummary hapmapValidate \
      illuminaLookup \
      illuminaLookup2 \
      illuminaLookup1M \
      snpCheckAlleles snpCheckClassAndObserved snpCheckCluster snpCheckCluster2 \
      snpClassAndObserved snpCleanSeq snpCompareLoctype snpCompareWeight \
      snpContigLocFilter snpContigLocFilter125 \
      snpContigLocusIdCondense snpContigLocusIdFilter snpContigLocusIdFilter125 \
      snpExpandAllele snpFinalTable snpFreq snpFunction \
      snpGetDeletions snpGetInsertions snpGetSeqDup snpGetSimple \
      snpLoadFasta snpLocType snpLocType125 \
      snpMissing snpMoltype snpMultiple \
      snpOrtho snpOrthoJoin \
      snpOrthoLookup snpPAR \
      snpReadFasta snpReadSeq snpReadSeq2 snpRefUCSC \
      snpSort snpSplitByChrom snpSplitByChrom2 snpSNP \
      subSnpCondense trimHeader
 
 affyLookup: affyLookup.o ${MYLIBS}
 	${CC} -O -o affyLookup affyLookup.o ${MYLIBS} $L
 
 cnpLookup: cnpLookup.o ${MYLIBS}
 	${CC} -O -o cnpLookup cnpLookup.o ${MYLIBS} $L
 
 fetchSeq: fetchSeq.o ${MYLIBS}
 	${CC} -O -o fetchSeq fetchSeq.o ${MYLIBS} $L
 
 hapmap1: hapmap1.o ${MYLIBS}
 	${CC} -O -o hapmap1 hapmap1.o ${MYLIBS} $L
 
 hapmap2: hapmap2.o ${MYLIBS}
 	${CC} -O -o hapmap2 hapmap2.o ${MYLIBS} $L
 
 hapmapLookup: hapmapLookup.o ${MYLIBS}
 	${CC} -O -o hapmapLookup hapmapLookup.o ${MYLIBS} $L
 
 hapmapMixed: hapmapMixed.o ${MYLIBS}
 	${CC} -O -o hapmapMixed hapmapMixed.o ${MYLIBS} $L
 
 hapmapOrtho: hapmapOrtho.o ${MYLIBS}
 	${CC} -O -o hapmapOrtho hapmapOrtho.o ${MYLIBS} $L
 
 hapmapSummary: hapmapSummary.o ${MYLIBS}
 	${CC} -O -o hapmapSummary hapmapSummary.o ${MYLIBS} $L
 
 hapmapValidate: hapmapValidate.o ${MYLIBS}
 	${CC} -O -o hapmapValidate hapmapValidate.o ${MYLIBS} $L
 
 illuminaLookup: illuminaLookup.o ${MYLIBS}
 	${CC} -O -o illuminaLookup illuminaLookup.o ${MYLIBS} $L
 
 illuminaLookup2: illuminaLookup2.o ${MYLIBS}
 	${CC} -O -o illuminaLookup2 illuminaLookup2.o ${MYLIBS} $L
 
 illuminaLookup1M: illuminaLookup1M.o ${MYLIBS}
 	${CC} -O -o illuminaLookup1M illuminaLookup1M.o ${MYLIBS} $L
 
 snpCheckAlleles: snpCheckAlleles.o ${MYLIBS}
 	${CC} -O -o snpCheckAlleles snpCheckAlleles.o ${MYLIBS} $L
 
 snpCheckClassAndObserved: snpCheckClassAndObserved.o ${MYLIBS}
 	${CC} -O -o snpCheckClassAndObserved snpCheckClassAndObserved.o ${MYLIBS} $L
 
 snpCheckCluster: snpCheckCluster.o ${MYLIBS}
 	${CC} -O -o snpCheckCluster snpCheckCluster.o ${MYLIBS} $L
 
 snpCheckCluster2: snpCheckCluster2.o ${MYLIBS}
 	${CC} -O -o snpCheckCluster2 snpCheckCluster2.o ${MYLIBS} $L
 
 snpClassAndObserved: snpClassAndObserved.o ${MYLIBS}
 	${CC} -O -o snpClassAndObserved snpClassAndObserved.o ${MYLIBS} $L
 
 snpCleanSeq: snpCleanSeq.o ${MYLIBS}
 	${CC} -O -o snpCleanSeq snpCleanSeq.o ${MYLIBS} $L
 
 snpCompareLoctype: snpCompareLoctype.o ${MYLIBS}
 	${CC} -O -o snpCompareLoctype snpCompareLoctype.o ${MYLIBS} $L
 
 snpCompareWeight: snpCompareWeight.o ${MYLIBS}
 	${CC} -O -o snpCompareWeight snpCompareWeight.o ${MYLIBS} $L
 
 snpContigLocFilter: snpContigLocFilter.o ${MYLIBS}
 	${CC} -O -o snpContigLocFilter snpContigLocFilter.o ${MYLIBS} $L
 
 snpContigLocFilter125: snpContigLocFilter125.o ${MYLIBS}
 	${CC} -O -o snpContigLocFilter125 snpContigLocFilter125.o ${MYLIBS} $L
 
 snpContigLocusIdCondense: snpContigLocusIdCondense.o ${MYLIBS}
 	${CC} -O -o snpContigLocusIdCondense snpContigLocusIdCondense.o ${MYLIBS} $L
 
 snpContigLocusIdFilter: snpContigLocusIdFilter.o ${MYLIBS}
 	${CC} -O -o snpContigLocusIdFilter snpContigLocusIdFilter.o ${MYLIBS} $L
 
 snpContigLocusIdFilter125: snpContigLocusIdFilter125.o ${MYLIBS}
 	${CC} -O -o snpContigLocusIdFilter125 snpContigLocusIdFilter125.o ${MYLIBS} $L
 
 snpExpandAllele: snpExpandAllele.o ${MYLIBS}
 	${CC} -O -o snpExpandAllele snpExpandAllele.o ${MYLIBS} $L
 
 snpFinalTable: snpFinalTable.o ${MYLIBS}
 	${CC} -O -o snpFinalTable snpFinalTable.o ${MYLIBS} $L
 
 snpFreq: snpFreq.o ${MYLIBS}
 	${CC} -O -o snpFreq snpFreq.o ${MYLIBS} $L
 
 snpFunction: snpFunction.o ${MYLIBS}
 	${CC} -O -o snpFunction snpFunction.o ${MYLIBS} $L
 
 snpGetDeletions: snpGetDeletions.o ${MYLIBS}
 	${CC} -O -o snpGetDeletions snpGetDeletions.o ${MYLIBS} $L
 
 snpGetInsertions: snpGetInsertions.o ${MYLIBS}
 	${CC} -O -o snpGetInsertions snpGetInsertions.o ${MYLIBS} $L
 
 snpGetSeqDup: snpGetSeqDup.o ${MYLIBS}
 	${CC} -O -o snpGetSeqDup snpGetSeqDup.o ${MYLIBS} $L
 
 snpGetSimple: snpGetSimple.o ${MYLIBS}
 	${CC} -O -o snpGetSimple snpGetSimple.o ${MYLIBS} $L
 
 snpLoadFasta: snpLoadFasta.o ${MYLIBS}
 	${CC} -O -o snpLoadFasta snpLoadFasta.o ${MYLIBS} $L
 
 snpLocType: snpLocType.o ${MYLIBS}
 	${CC} -O -o snpLocType snpLocType.o ${MYLIBS} $L
 
 snpLocType125: snpLocType125.o ${MYLIBS}
 	${CC} -O -o snpLocType125 snpLocType125.o ${MYLIBS} $L
 
 snpMissing: snpMissing.o ${MYLIBS}
 	${CC} -O -o snpMissing snpMissing.o ${MYLIBS} $L
 
 snpMoltype: snpMoltype.o ${MYLIBS}
 	${CC} -O -o snpMoltype snpMoltype.o ${MYLIBS} $L
 
 snpMultiple: snpMultiple.o ${MYLIBS}
 	${CC} -O -o snpMultiple snpMultiple.o ${MYLIBS} $L
 
 snpOrtho: snpOrtho.o ${MYLIBS}
 	${CC} -O -o snpOrtho snpOrtho.o ${MYLIBS} $L
 
 snpOrthoJoin: snpOrthoJoin.o ${MYLIBS}
 	${CC} -O -o snpOrthoJoin snpOrthoJoin.o ${MYLIBS} $L
 
 snpOrthoLookup: snpOrthoLookup.o ${MYLIBS}
 	${CC} -O -o snpOrthoLookup snpOrthoLookup.o ${MYLIBS} $L
 
 snpPAR: snpPAR.o ${MYLIBS}
 	${CC} -O -o snpPAR snpPAR.o ${MYLIBS} $L
 
 snpReadFasta: snpReadFasta.o ${MYLIBS}
 	${CC} -O -o snpReadFasta snpReadFasta.o ${MYLIBS} $L
 
 snpReadSeq: snpReadSeq.o ${MYLIBS}
 	${CC} -O -o snpReadSeq snpReadSeq.o ${MYLIBS} $L
 
 snpReadSeq2: snpReadSeq2.o ${MYLIBS}
 	${CC} -O -o snpReadSeq2 snpReadSeq2.o ${MYLIBS} $L
 
 snpRefUCSC: snpRefUCSC.o ${MYLIBS}
 	${CC} -O -o snpRefUCSC snpRefUCSC.o ${MYLIBS} $L
 
 snpSort: snpSort.o ${MYLIBS}
 	${CC} -O -o snpSort snpSort.o ${MYLIBS} $L
 
 snpSplitByChrom: snpSplitByChrom.o ${MYLIBS}
 	${CC} -O -o snpSplitByChrom snpSplitByChrom.o ${MYLIBS} $L
 
 snpSplitByChrom2: snpSplitByChrom2.o ${MYLIBS}
 	${CC} -O -o snpSplitByChrom2 snpSplitByChrom2.o ${MYLIBS} $L
 
 snpSNP: snpSNP.o ${MYLIBS}
 	${CC} -O -o snpSNP snpSNP.o ${MYLIBS} $L
 
 subSnpCondense: subSnpCondense.o ${MYLIBS}
 	${CC} -O -o subSnpCondense subSnpCondense.o ${MYLIBS} $L
 
 trimHeader: trimHeader.o ${MYLIBS}
 	${CC} -O -o trimHeader trimHeader.o ${MYLIBS} $L