@@ -319,7 +319,7 @@ fit.wls <- function(NN, sigma, allele, Y, autosome, X){

 shrinkGenotypeSummaries <- function(strata, index.list, object, MIN.OBS, MIN.SAMPLES, DF.PRIOR,

 				    verbose, is.lds){

 	if(is.lds) {physical <- get("physical"); open(object)}

-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))

+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))

 	marker.index <- index.list[[strata]]

 	batches <- split(seq_along(batch(object)), as.character(batch(object)))

 	batches <- batches[sapply(batches, length) >= MIN.SAMPLES]

@@ -455,7 +455,7 @@ fit.lm1 <- function(strata,

 		    verbose, is.lds,

 		    CHR.X, ...){

 	if(is.lds) {physical <- get("physical"); open(object)}

-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))

+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))

 	snps <- index.list[[strata]]

 	batches <- split(seq_along(batch(object)), as.character(batch(object)))

 	batches <- batches[sapply(batches, length) >= MIN.SAMPLES]

@@ -535,7 +535,7 @@ fit.lm2 <- function(strata,

 		    MIN.PHI,

 		    verbose, is.lds, CHR.X, ...){

 	if(is.lds) {physical <- get("physical"); open(object)}

-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))

+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))

 	marker.index <- index.list[[strata]]

 	batches <- split(seq_along(batch(object)), as.character(batch(object)))

 	batches <- batches[sapply(batches, length) >= MIN.SAMPLES]

@@ -717,7 +717,7 @@ fit.lm3 <- function(strata,

 		    MIN.PHI,

 		    verbose, is.lds, CHR.X, ...){

 	if(is.lds) {physical <- get("physical"); open(object)}

-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))

+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))

 	gender <- object$gender

 	enough.males <- sum(gender==1) > MIN.SAMPLES

 	enough.females <- sum(gender==2) > MIN.SAMPLES

@@ -879,7 +879,7 @@ fit.lm4 <- function(strata,

 		message(paste("fewer than", MIN.SAMPLES, "men and women.  Copy number not estimated for CHR X"))

 		return(object)

 	}

-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))

+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))

 	marker.index <- index.list[[strata]]

 	batches <- split(seq_along(batch(object)), as.character(batch(object)))

 	batches <- batches[sapply(batches, length) >= MIN.SAMPLES]

@@ -1396,7 +1396,7 @@ whichMarkers <- function(type, is.snp, is.autosome, is.annotated, is.X){

 summarizeNps <- function(strata, index.list, object, batchSize,

 			 GT.CONF.THR, verbose, is.lds, CHR.X, ...){

 	if(is.lds) {physical <- get("physical"); open(object)}

-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))

+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))

 	index <- index.list[[strata]]

 	if(CHR.X) {

 		sample.index <- which(object$gender==2)

@@ -1449,7 +1449,7 @@ summarizeSnps <- function(strata,

 		physical <- get("physical")

 		open(object)

 	}

-	if(verbose) message("Probe stratum ", strata, " of ", length(index.list))

+	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))

 	index <- index.list[[strata]]

 ##	if(CHR.X) {

 ##		sample.index <- which(object$gender==2)