From: Bo Li <bli@cs.wisc.edu>
Date: Fri, 18 Mar 2011 18:31:33 +0000 (-0500)
Subject: v1.1.5.b
X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=e123915d329682a1712bf77204e556baadb69a2f

v1.1.5.b
---

diff --git a/README.md b/README.md
index b95c4ea..0f96f69 100644
--- a/README.md
+++ b/README.md
@@ -136,10 +136,18 @@ outF: the file name for plots generated from the model. It is a pdf file
 
 The plots generated depends on read type and user configuration. It
 may include fragment length distribution, mate length distribution,
-read start position distribution (RSPD), quality score vs percentage
-of sequecing error given the reference base, position vs percentage of
-sequencing error given the reference base.
+read start position distribution (RSPD), quality score vs observed
+quality given a reference base, position vs percentage of sequencing
+error given a reference base.
 
+fragment length distribution and mate length distribution: x-axis is fragment/mate length, y axis is the probability of generating a fragment/mate with the associated length
+
+RSPD: Read Start Position Distribution. x-axis is bin number, y-axis is the probability of each bin. RSPD can be used as an indicator of 3' bias
+
+Quality score vs. observed quality given a reference base: x-axis is Phred quality scores associated with data, y-axis is the "observed quality", Phred quality scores learned by RSEM from the data. Q = -10log_10(P), where Q is Phred quality score and P is the probability of sequencing error for a particular base
+
+Position vs. percentage sequencing error given a reference base: x-axis is position and y-axis is percentage sequencing error
+ 
 ## <a name="example"></a> Example
 
 Suppose we download the mouse genome from UCSC Genome Browser.  We will
diff --git a/calcCI.cpp b/calcCI.cpp
index d1f26e5..321cd4a 100644
--- a/calcCI.cpp
+++ b/calcCI.cpp
@@ -378,7 +378,7 @@ int main(int argc, char* argv[]) {
 
 	delete[] tau_denoms;
 
-	sprintf(command, "rm -f %s", tmpF);
+       	sprintf(command, "rm -f %s", tmpF);
 	int status = system(command);
 	if (status != 0) {
 	  fprintf(stderr, "Cannot delete %s!\n", tmpF);
diff --git a/rsem-plot-model b/rsem-plot-model
index c0eaa1b..333a9e7 100755
--- a/rsem-plot-model
+++ b/rsem-plot-model
@@ -96,10 +96,10 @@ if (model_type == 1 || model_type == 3) {
     vecG <- as.numeric(list[[3]])
     vecT <- as.numeric(list[[4]])
     if (sum(c(vecA, vecC, vecG, vecT)) < 1e-8) break
-    peA <- c(peA, ifelse(sum(vec) < 1e-8, NA, 1.0 - vecA[1]))
-    peC <- c(peC, ifelse(sum(vec) < 1e-8, NA, 1.0 - vecC[2]))
-    peG <- c(peG, ifelse(sum(vec) < 1e-8, NA, 1.0 - vecG[3]))
-    peT <- c(peT, ifelse(sum(vec) < 1e-8, NA, 1.0 - vecT[4]))
+    peA <- c(peA, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecA[1]) * 100))
+    peC <- c(peC, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecC[2]) * 100))
+    peG <- c(peG, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecG[3]) * 100))
+    peT <- c(peT, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecT[4]) * 100))
   }
 
   x <- 1 : length(peA)