rsem v1.1.15

diff --git a/BamConverter.h b/BamConverter.h
index 9b543087443aac68a72999a13e874b199d613cc4..cca0eae895fd347b243cc8f2f315be471c64498c 100644 (file)
--- a/BamConverter.h
+++ b/BamConverter.h
@@ -91,7 +91,7 @@ void BamConverter::process() {
                if (cnt % 1000000 == 0) { printf("."); fflush(stdout); }
 
                // at least one segment is not properly mapped
-               if ((b->core.flag & 0x0004) || isPaired && (b2->core.flag & 0x0004)) continue;
+               if ((b->core.flag & 0x0004) || (isPaired && (b2->core.flag & 0x0004))) continue;
 
                const Transcript& transcript = transcripts.getTranscriptAt(b->core.tid + 1);
 

diff --git a/FOR_CYGWIN_USERS b/FOR_CYGWIN_USERS
new file mode 100644 (file)
index 0000000..b743e81
--- /dev/null
+++ b/FOR_CYGWIN_USERS
@@ -0,0 +1 @@
+Please uncomment the 4th and 8th lines in sam/Makefile before compiling RSEM.

diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
new file mode 100644 (file)
index 0000000..2a6cc2f
--- /dev/null
+++ b/WHAT_IS_NEW
@@ -0,0 +1,17 @@
+
+RSEM v1.1.15
+
+- Fixed several bugs causing compilation error
+- Modified samtools' Makefile for cygwin. For cygwin users, please uncomment the 4th and 8th lines in sam/Makefile before compiling RSEM
+
+--------------------------------------------------------------------------------------------
+RSEM v1.1.14
+
+- Added --chunkmbs option to rsem-calculate-expression (patch contributed by earonesty)
+- Added --sampling-for-bam option to rsem-calculate-expression, in the bam file, instead of providing expected weights, for each read RSEM samples one alignment based on the expected weights
+- RSEM can generate BAM and Wiggle files in both genomic-coordinate and transcript-coordinate
+- Added rsem-plot-transcript-wiggles. This script can generate transcript-coordinate wiggle plots in pdf format. One unique feature is, a stacked plot can be generated, with unique read contribution shown as black and multi-read contribution shown as red
+- Added convert_sam_for_rsem script for users do not use bowtie aligner
+- Modified RSEM's GTF file parser. Now RSEM does not require "transcript_id" and "gene_id" be the first two attributes shown
+- Improved descriptions for thread related errors 
+

diff --git a/bam2readdepth.cpp b/bam2readdepth.cpp
index c7f0adbcecc96bfaab0a24b5fa4764d27cd2e268..87fb178a60ad08c146cb6b23e3979e4237cdd480 100644 (file)
--- a/bam2readdepth.cpp
+++ b/bam2readdepth.cpp
@@ -1,13 +1,20 @@
+#include <cstdio>
+#include <cstring>
+#include <cstdlib>
 #include <iostream>
+
 #include "wiggle.h"
 
+using namespace std;
+
 int main(int argc, char* argv[]) {
-       if (argc != 2) {
-               printf("Usage: rsem-bam2readdepth sorted_bam_input\n");
-        std::exit(1);
-       }
+  if (argc != 2) {
+    printf("Usage: rsem-bam2readdepth sorted_bam_input\n");
+    exit(-1);
+  }
+
     ReadDepthWriter depth_writer(std::cout);
     build_wiggles(argv[1], depth_writer);
 
-       return 0;
+    return 0;
 }

diff --git a/bam2wig.cpp b/bam2wig.cpp
index b03d0b32e10eb8991f171dec1892a76a66fb9cd7..24a53c60d48b478fc06677f61846af9c8c92f64a 100644 (file)
--- a/bam2wig.cpp
+++ b/bam2wig.cpp
@@ -1,4 +1,6 @@
 #include <cstdio>
+#include <cstdlib>
+#include <cstring>
 
 #include "wiggle.h"
 

diff --git a/bc_aux.h b/bc_aux.h
index 0527e7eecd6b1dd32c6e99b5dd4fea3fbd400e2e..eb1f1a0130a5958e7822156dc1119d5c0ccd0aed 100644 (file)
--- a/bc_aux.h
+++ b/bc_aux.h
@@ -46,7 +46,7 @@ struct PairedEndT {
 
        bool operator< (const PairedEndT& o) const {
                int value = mate1.compare(o.mate1);
-               return value < 0 || value == 0 && mate2 < o.mate2;
+               return value < 0 || (value == 0 && mate2 < o.mate2);
        }
 };
 

diff --git a/getUnique.cpp b/getUnique.cpp
index 8e2ba4e17e58a9eb95837a8343b3831d1b3973b2..7272a810ca528f330a8b3ddb6efa12c090746b4e 100644 (file)
--- a/getUnique.cpp
+++ b/getUnique.cpp
@@ -20,7 +20,7 @@ bool unaligned;
 void output() {
        if (unaligned || arr.size() == 0) return;
        bool isPaired = (arr[0]->core.flag & 0x0001);
-       if (isPaired && arr.size() != 2 || !isPaired && arr.size() != 1) return;
+       if ((isPaired && arr.size() != 2) || (!isPaired && arr.size() != 1)) return;
        for (int i = 0; i < (int)arr.size(); i++) samwrite(out, arr[i]);
 }
 

diff --git a/sam/Makefile b/sam/Makefile
index db183330d1fb76ce4fa0d17d8dab65afdfbeb65a..bb89e00da2ed01bf2a44ff488f911ac528f32a62 100644 (file)
--- a/sam/Makefile
+++ b/sam/Makefile
@@ -1,6 +1,13 @@
 CC=                    gcc
-CFLAGS=                -g -Wall -O2 #-m64 #-arch ppc
-DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
+
+CFLAGS_EXTRA=
+#CFLAGS_EXTRA= -L/usr/include/ncurses
+CFLAGS=                -g -Wall -O2 $(CFLAGS_EXTRA) #-m64 #-arch ppc
+
+DFLAGS_EXTRA=
+#DFLAGS_EXTRA= -Dexpl=exp -Dlogl=log
+DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 $(DFLAGS_EXTRA)
+
 KNETFILE_O=    knetfile.o
 LOBJS=         bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
                        bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \

diff --git a/simulation.cpp b/simulation.cpp
index e516cc15c32848e143aaf4b3a56a1e738fbe3456..e0c9cec83c1891ee9e5ec099602c94fe024ef9d3 100644 (file)
--- a/simulation.cpp
+++ b/simulation.cpp
@@ -237,7 +237,7 @@ int main(int argc, char* argv[]) {
        //read model type from modelF
        fi = fopen(argv[2], "r");
        if (fi == NULL) { fprintf(stderr, "Cannot open %s! It may not exist.\n", argv[2]); exit(-1); }
-       fscanf(fi, "%d", &model_type);
+       assert(fscanf(fi, "%d", &model_type) == 1);
        fclose(fi);
 
        theta = new double[M + 1];

diff --git a/what_is_new b/what_is_new
deleted file mode 100644 (file)
index 7168193..0000000
--- a/what_is_new
+++ /dev/null
@@ -1,10 +0,0 @@
-In this version of RSEM, several things are updated:
-
-- Added --chunkmbs option to rsem-calculate-expression (patch contributed by earonesty)
-- Added --sampling-for-bam option to rsem-calculate-expression, in the bam file, instead of providing expected weights, for each read RSEM samples one alignment based on the expected weights
-- RSEM can generate BAM and Wiggle files in both genomic-coordinate and transcript-coordinate
-- Added rsem-plot-transcript-wiggles. This script can generate transcript-coordinate wiggle plots in pdf format. One unique feature is, a stacked plot can be generated, with unique read contribution shown as black and multi-read contribution shown as red
-- Added convert_sam_for_rsem script for users do not use bowtie aligner
-- Modified RSEM's GTF file parser. Now RSEM does not require "transcript_id" and "gene_id" be the first two attributes shown
-- Improved descriptions for thread related errors. 
-