From 4892b3ff2bdcdf45fb7e43d46122df572dd31510 Mon Sep 17 00:00:00 2001
From: "Stephanie M. Gogarten" <sdmorris@uw.edu>
Date: Thu, 18 Apr 2019 18:52:23 -0700
Subject: [PATCH] bug fix for one sample block in pcrelate

---
 R/pcrelate.R | 33 +++++++++++++++++++--------------
 pcrelate.py  |  7 +++++--
 2 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/R/pcrelate.R b/R/pcrelate.R
index acfc7eb4..67951578 100644
--- a/R/pcrelate.R
+++ b/R/pcrelate.R
@@ -53,21 +53,26 @@ iterator <- SeqVarBlockIterator(seqData, variantBlock=block.size)
 # create sample blocks
 #nsampblock <- ceiling(length(sample.include)/sample.block.size)
 nsampblock <- as.integer(config["n_sample_blocks"])
-samp.blocks <- unname(split(sample.include, cut(1:length(sample.include), nsampblock)))
+if (nsampblock > 1) {
+    samp.blocks <- unname(split(sample.include, cut(1:length(sample.include), nsampblock)))
 
-# map segment number to sample block numbers
-## jobs <- list()
-## s <- 1
-## for (i in 1:nsampblock) {
-##     for (j in i:nsampblock) {
-##         jobs[[s]] <- c(i,j)
-##         s <- s + 1
-##     }
-## }
-jobs <- c(combn(1:nsampblock, 2, simplify=FALSE),
-          lapply(1:nsampblock, function(x) c(x,x)))
-i <- jobs[[segment]][1]
-j <- jobs[[segment]][2]
+    # map segment number to sample block numbers
+    ## jobs <- list()
+    ## s <- 1
+    ## for (i in 1:nsampblock) {
+    ##     for (j in i:nsampblock) {
+    ##         jobs[[s]] <- c(i,j)
+    ##         s <- s + 1
+    ##     }
+    ## }
+    jobs <- c(combn(1:nsampblock, 2, simplify=FALSE),
+              lapply(1:nsampblock, function(x) c(x,x)))
+    i <- jobs[[segment]][1]
+    j <- jobs[[segment]][2]
+} else {
+    samp.blocks <- list(sample.include)
+    i <- j <- 1
+}
 
 out <- pcrelateSampBlock(iterator,
                          betaobj=beta,
diff --git a/pcrelate.py b/pcrelate.py
index 8d24eb37..8de3c433 100755
--- a/pcrelate.py
+++ b/pcrelate.py
@@ -76,8 +76,11 @@
 
 # define sample blocks
 n_blocks = int(configdict.setdefault("n_sample_blocks", "1"))
-blocks = [(i,j) for i in range(1, n_blocks+1) for j in range(i, n_blocks+1)]
-block_range = "1-" + str(len(blocks))
+if n_blocks > 1:
+    blocks = [(i,j) for i in range(1, n_blocks+1) for j in range(i, n_blocks+1)]
+    block_range = "1-" + str(len(blocks))
+else:
+    block_range = "1"
 
 jobid = cluster.submitJob(job_name=job, cmd=driver, args=["-s", rscript, configfile, version], holdid=[jobid], array_range=block_range, email=email, print_only=print_only)