From: Bo Li Date: Thu, 26 Jan 2012 22:23:20 +0000 (-0600) Subject: rsem v1.1.15 X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=0a534802ee9fa3d488995a68621ff04f0fc6be7f rsem v1.1.15 --- diff --git a/BamConverter.h b/BamConverter.h index 9b54308..cca0eae 100644 --- 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 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 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 c7f0adb..87fb178 100644 --- a/bam2readdepth.cpp +++ b/bam2readdepth.cpp @@ -1,13 +1,20 @@ +#include +#include +#include #include + #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 b03d0b3..24a53c6 100644 --- a/bam2wig.cpp +++ b/bam2wig.cpp @@ -1,4 +1,6 @@ #include +#include +#include #include "wiggle.h" diff --git a/bc_aux.h b/bc_aux.h index 0527e7e..eb1f1a0 100644 --- 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 8e2ba4e..7272a81 100644 --- 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 db18333..bb89e00 100644 --- 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 e516cc1..e0c9cec 100644 --- 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 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. -