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Makefile
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Makefile
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CC = gcc
CFLAGS = -O3 -Wall -lm
msMask: msMask.c
$(CC) msMask.c -o msMask $(CFLAGS)
msMaskAllRows: msMaskAllRows.c
$(CC) msMaskAllRows.c -o msMaskAllRows $(CFLAGS)
maskedStats: maskedStats.c msGeneralStats.c
$(CC) maskedStats.c msGeneralStats.c -o maskedStats $(CFLAGS)
niceStatsDan: niceStatsDan.c msGeneralStats.c
$(CC) niceStatsDan.c msGeneralStats.c -g -o niceStatsDan $(CFLAGS)
niceStatsSFSRegular: niceStatsSFSRegular.c msGeneralStats.c
$(CC) niceStatsSFSRegular.c msGeneralStats.c -g -o niceStatsSFSRegular $(CFLAGS)
niceStats: niceStats.c msGeneralStats.c
$(CC) niceStats.c msGeneralStats.c -o niceStats $(CFLAGS)
maskedStatsSubpop: maskedStatsSubpop.c msGeneralStats.c
$(CC) maskedStatsSubpop.c msGeneralStats.c -o maskedStatsSubpop $(CFLAGS)
twoPopnNiceStats: twoPopnNiceStats.c msGeneralStats.c
$(CC) twoPopnNiceStats.c msGeneralStats.c -o twoPopnNiceStats $(CFLAGS)
twoPopnStats_forML: twoPopnStats_forML.c msGeneralStats.c
$(CC) twoPopnStats_forML.c msGeneralStats.c -o twoPopnStats_forML $(CFLAGS)
onePopnStats_forGhostIntroML: onePopnStats_forGhostIntroML.c msGeneralStats.c
$(CC) onePopnStats_forGhostIntroML.c msGeneralStats.c -o onePopnStats_forGhostIntroML $(CFLAGS)
threePopnStats: threePopnStats.c msGeneralStats.c
$(CC) threePopnStats.c msGeneralStats.c -o threePopnStats $(CFLAGS)
msParams: msParams.c
$(CC) msParams.c ../coalLib/ranlibComplete.c ../pgLib/bedFile.c -o msParams $(CFLAGS)
msParamsSubpop: msParamsSubpop.c
$(CC) msParamsSubpop.c ../coalLib/ranlibComplete.c ../pgLib/bedFile.c -o msParamsSubpop $(CFLAGS)
msParamsSubpopNoAd: msParamsSubpopNoAd.c
$(CC) msParamsSubpopNoAd.c ../coalLib/ranlibComplete.c ../pgLib/bedFile.c -o msParamsSubpopNoAd $(CFLAGS)
msParamsSubpopTrans: msParamsSubpopTrans.c
$(CC) msParamsSubpopTrans.c ../coalLib/ranlibComplete.c ../pgLib/bedFile.c -o msParamsSubpopTrans $(CFLAGS)
msParamsTest: msParamsTest.c
$(CC) msParamsTest.c ../coalLib/ranlibComplete.c ../pgLib/bedFile.c -o msParamsTest $(CFLAGS)
pairDist: pairDist.c msGeneralStats.c
$(CC) pairDist.c msGeneralStats.c -o pairDist $(CFLAGS)
pairwiseDists: pairwiseDists.c msGeneralStats.c
$(CC) pairwiseDists.c msGeneralStats.c -o pairwiseDists $(CFLAGS)
pairwiseIBSTracts: pairwiseIBSTracts.c msGeneralStats.c
$(CC) pairwiseIBSTracts.c msGeneralStats.c -o pairwiseIBSTracts $(CFLAGS)
msHKA: msHKA.c msGeneralStats.c
$(CC) msHKA.c msGeneralStats.c -o msHKA $(CFLAGS)
ms2TwoSite: ms2TwoSite.c msGeneralStats.c
$(CC) ms2TwoSite.c msGeneralStats.c -o ms2TwoSite $(CFLAGS)
ms2RSquareByDistance: ms2RSquareByDistance.c msGeneralStats.c
$(CC) ms2RSquareByDistance.c msGeneralStats.c -o ms2RSquareByDistance $(CFLAGS)
ms2TwoSite2Popn: ms2TwoSite2Popn.c msGeneralStats.c
$(CC) ms2TwoSite2Popn.c msGeneralStats.c -o ms2TwoSite2Popn $(CFLAGS)
ms2SFS2D: ms2SFS2D.c msGeneralStats.c
$(CC) ms2SFS2D.c msGeneralStats.c -o ms2SFS2D $(CFLAGS)
ms2SFS2D_discoal: ms2SFS2D_discoal.c msGeneralStats.c
$(CC) ms2SFS2D_discoal.c msGeneralStats.c -o ms2SFS2D_discoal $(CFLAGS)
ms2SFSVector: ms2SFSVector.c msGeneralStats.c
$(CC) ms2SFSVector.c msGeneralStats.c -o ms2SFSVector $(CFLAGS)
ms2SFSVectorWindow: ms2SFSVectorWindow.c msGeneralStats.c
$(CC) ms2SFSVectorWindow.c msGeneralStats.c -o ms2SFSVectorWindow $(CFLAGS)
discoal_mig2hmm: discoal_mig2hmm.c msGeneralStats.c
$(CC) discoal_mig2hmm.c msGeneralStats.c -o discoal_mig2hmm $(CFLAGS)
slideFST: slideFST.c msGeneralStats.c
$(CC) slideFST.c msGeneralStats.c -o slideFST $(CFLAGS)
niceStatsNoOmega: niceStatsNoOmega.c msGeneralStats.c
$(CC) niceStatsNoOmega.c msGeneralStats.c -g -o niceStatsNoOmega $(CFLAGS)
niceStatsShanku: niceStatsShanku.c msGeneralStats.c
$(CC) niceStatsShanku.c msGeneralStats.c -o niceStatsShanku $(CFLAGS)
niceStatsAchazSystem: niceStatsAchazSystem.c msGeneralStats.c
$(CC) niceStatsAchazSystem.c msGeneralStats.c -O3 -o niceStatsAchazSystem $(CFLAGS)
niceStatsDiploid: niceStatsDiploid.c msGeneralStats.c msDiploidStats.c
$(CC) niceStatsDiploid.c msGeneralStats.c msDiploidStats.c -o niceStatsDiploid $(CFLAGS)
niceStats4Gamete: niceStats4Gamete.c msGeneralStats.c
$(CC) niceStats4Gamete.c msGeneralStats.c -o niceStats4Gamete $(CFLAGS)