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Makefile
View file @ 01ffd309
......@@ -5,8 +5,8 @@ endif
CC = g++
EXEC = e-mem
CFLAGS = -Wall -Wextra -Wunused -mpopcnt -std=gnu++0x -fopenmp
CDEBUG = -g -ggdb -DDEBUG
CPROF = -g -ggdb -DDEBUG -pg
CDEBUG = -g -ggdb -gdwarf-3 -DDEBUG
CPROF = -g -ggdb -gdwarf-3 -DDEBUG -pg
COPTIMIZE = -Wuninitialized -O3 -fomit-frame-pointer
CLIBS = -lm
......
README.md
View file @ 01ffd309
......@@ -15,7 +15,29 @@ E-MEM is an efficient MEM computation program for large genomes which can be use
OUTPUT:
stdout a list of exact matches
The E-MEM program prints maximal exact matches on standard output. The output format varies depending on the command line options used. In the default mode 3-column output is printed. The option -b allows printing of matches in both forward and reverse complement directions. Below is the description of the output format with respect to the example included with e-mem program. For each query sequence, the sequence name or ID is reported on the first line followed by a '>' character. The sequence name will be reported even if there are no MEMs found for this sequence. For example, the query sequence in 'Reverse' reports sequence name with no matching MEMs. Note that, for each query sequence, the reverse complemented MEMs immediately follow the forward MEMs. For each match, the 3-columns list the start position in the reference sequence, the start position in the query sequence, and the length of the match respectively. For reverse matches, the positions are reported relative to the reverse query sequence. The option -c is used to report reverse match positions with respect to forward query sequence.
> gi|5524211|gb|AAD44166.1|
4 1 51
8 1 51
12 1 51
16 1 51
20 1 51
24 1 51
28 1 51
1 2 50
> gi|5524211|gb|AAD44166.1| Reverse
The 3-column output is sufficient for reporting matches between one reference sequence and one/more query sequences. For multiple reference sequences, 4-column output is desired. E-MEM provides an option -F to print 4-column output which also prints the reference sequence name/ID for each match. Below is a dummy example of 4-column output. The first column now indicates the name/ID of the reference sequence followed by the 3-column output format as described above.
> gi|5524211|gb|AAD44166.1|
ref1 4 1 51
ref1 8 1 51
ref2 12 1 51
ref2 16 1 51
ref3 20 1 51
ref3 24 1 51
##-- INSTALLATION --
......@@ -69,7 +91,7 @@ For example, in order to use NUCMER (all-vs-all comparison of nucleotide sequenc
The other important script in MUmmer3 is run-mummer3 (the alignment program). To use this script with E-MEM, simply replace "$bindir/mummer" with "< path >/e-mem" where < path > is e-mem installation directory.
###CITE
## CITE
If you find E-MEM program useful, please cite the E-MEM paper:
N. Khiste, L. Ilie [E-MEM: efficient computation of maximal exact matches for very large genomes](http://bioinformatics.oxfordjournals.org/content/31/4/509.short) Bioinformatics, 2015
......
debian/changelog
View file @ 01ffd309
e-mem (1.0.1-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.1.3
* debhelper 11
-- Andreas Tille <tille@debian.org> Thu, 15 Feb 2018 16:45:11 +0100
e-mem (1.0.0-1) unstable; urgency=medium
* New upstream version available from Github
......
debian/control
View file @ 01ffd309
......@@ -3,9 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
libboost-dev
Standards-Version: 3.9.8
Standards-Version: 4.1.3
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/e-mem.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/e-mem.git
Homepage: http://www.csd.uwo.ca/~ilie/E-MEM/
......
debian/patches/hardening.patch
View file @ 01ffd309
......@@ -10,8 +10,8 @@ Description: Propagate hardening options
EXEC = e-mem
-CFLAGS = -Wall -Wextra -Wunused -mpopcnt -std=gnu++0x -fopenmp
+CFLAGS += -Wall -Wextra -Wunused -mpopcnt -std=gnu++0x -fopenmp
CDEBUG = -g -ggdb -DDEBUG
CPROF = -g -ggdb -DDEBUG -pg
CDEBUG = -g -ggdb -gdwarf-3 -DDEBUG
CPROF = -g -ggdb -gdwarf-3 -DDEBUG -pg
COPTIMIZE = -Wuninitialized -O3 -fomit-frame-pointer
@@ -36,7 +36,7 @@ profile: all
......
debian/patches/remove_unused_mpopcnt_option.patch
View file @ 01ffd309
......@@ -18,6 +18,6 @@ Description: Software in Debian is supposed to run on the baseline of the
EXEC = e-mem
-CFLAGS += -Wall -Wextra -Wunused -mpopcnt -std=gnu++0x -fopenmp
+CFLAGS += -Wall -Wextra -Wunused -std=gnu++0x -fopenmp
CDEBUG = -g -ggdb -DDEBUG
CPROF = -g -ggdb -DDEBUG -pg
CDEBUG = -g -ggdb -gdwarf-3 -DDEBUG
CPROF = -g -ggdb -gdwarf-3 -DDEBUG -pg
COPTIMIZE = -Wuninitialized -O3 -fomit-frame-pointer
e-mem.cpp
View file @ 01ffd309
......@@ -234,6 +234,14 @@ void helperReportMem(uint64_t &currRPos, uint64_t &currQPos, uint64_t totalRBits
rQue-=2;
break;
}
/* if current rRef/rQue plus matchSize smaller than minMEMLength, then simply return.
* Note that one less character is compared due to a mismatch
*/
if (rRef+matchSize-lRef < static_cast<uint64_t>(commonData::minMemLen))
{
return;
}
mismatch=1;
matchSize/=2;
if (matchSize%2)
......@@ -488,7 +496,7 @@ void checkCommandLineOptions(uint32_t &options)
void print_help_msg()
{
cout << endl;
cout << "E-MEM Version 1.0.0, Sep. 25, 2014" << endl;
cout << "E-MEM Version 1.0.1, Dec. 12, 2017" << endl;
cout << "© 2014 Nilesh Khiste, Lucian Ilie" << endl;
cout << endl;
cout << "E-MEM finds and outputs the position and length of all maximal" << endl;
......@@ -739,6 +747,7 @@ int main (int argc, char *argv[])
QueryFile.closeFile();
arrayTmpFile.removeDuplicates(refSeqInfo, querySeqInfo, revComplement);
fflush(0);
return 0;
}
file.h
View file @ 01ffd309
......@@ -278,7 +278,7 @@ class seqFileReadInfo {
{
size = size/commonData::d;
binReadSize = floor((size+numSequences*RANDOM_SEQ_SIZE+commonData::d)/32+4);
binReads = new uint64_t[binReadSize];
binReads = new uint64_t[binReadSize+1];
return size;
}
......@@ -495,7 +495,7 @@ class seqFileReadInfo {
void writeReverseComplementString(string &name, string &content, fstream &file)
{
file << ">" << name << endl;
file << ">" << name << "\n";
flipNswap(content);
file << content ;
}
......@@ -747,15 +747,15 @@ class tmpFilesInfo {
{
if (revComplement & 0x1){
if (commonData::lenInHeader) {
cout << "> " << (*itQ).seq << " Reverse" << " Len = " << ((*itQ).end-(*itQ).start+2)/2 << endl;
cout << "> " << (*itQ).seq << " Reverse" << " Len = " << ((*itQ).end-(*itQ).start+2)/2 << "\n";
}else{
cout << "> " << (*itQ).seq << " Reverse" << endl;
cout << "> " << (*itQ).seq << " Reverse" << "\n";
}
}else{
if (commonData::lenInHeader){
cout << "> " << (*itQ).seq << " Len = " << ((*itQ).end-(*itQ).start+2)/2 << endl;
cout << "> " << (*itQ).seq << " Len = " << ((*itQ).end-(*itQ).start+2)/2 << "\n";
}else{
cout << "> " << (*itQ).seq << endl;
cout << "> " << (*itQ).seq << "\n";
}
}
}
......@@ -873,14 +873,14 @@ class tmpFilesInfo {
if (rRef-lRef+2 >= static_cast<uint64_t>(commonData::minMemLen)){
if (refSeqInfo.size() == 1 && !commonData::fourColOutput) {
if ((revComplement & 0x1) && commonData::relQueryPos)
cout << " " << setw(15) << ((lRef+2)/2) << setw(15) << ((*itQ).end-(*itQ).start-lQue+2)/2 << setw(15) << ((rRef-lRef+2)/2) << endl;
cout << " " << setw(15) << ((lRef+2)/2) << setw(15) << ((*itQ).end-(*itQ).start-lQue+2)/2 << setw(15) << ((rRef-lRef+2)/2) << "\n";
else
cout << " " << setw(15) << ((lRef+2)/2) << setw(15) << ((lQue+2)/2) << setw(15) << ((rRef-lRef+2)/2) << endl;
cout << " " << setw(15) << ((lRef+2)/2) << setw(15) << ((lQue+2)/2) << setw(15) << ((rRef-lRef+2)/2) << "\n";
}else{
if ((revComplement & 0x1) && commonData::relQueryPos) {
cout << " " << setw(30) << std::left <<(*itR).seq << setw(15) << ((lRef+2)/2) << setw(15) << ((*itQ).end-(*itQ).start-lQue+2)/2 << setw(15) << ((rRef-lRef+2)/2) << endl;
cout << " " << setw(30) << std::left <<(*itR).seq << setw(15) << ((lRef+2)/2) << setw(15) << ((*itQ).end-(*itQ).start-lQue+2)/2 << setw(15) << ((rRef-lRef+2)/2) << "\n";
}else{
cout << " " << setw(30) << std::left <<(*itR).seq << setw(15) << ((lRef+2)/2) << setw(15) << ((lQue+2)/2) << setw(15) << ((rRef-lRef+2)/2) << endl;
cout << " " << setw(30) << std::left <<(*itR).seq << setw(15) << ((lRef+2)/2) << setw(15) << ((lQue+2)/2) << setw(15) << ((rRef-lRef+2)/2) << "\n";
}
}
}
......@@ -959,31 +959,31 @@ class tmpFilesInfo {
filePtr = forFile;
if(getline((*filePtr), line).good())
cout << line << endl;
cout << line << "\n";
while(getline((*filePtr), line).good()) {
if(line[0] == '>'){
if (last_line.size())
cout << last_line << endl;
cout << last_line << "\n";
last_line = line;
if (filePtr == forFile) {
filePtr = revFile;
if (first) {
if(getline((*filePtr), line).good())
cout << line << endl;
cout << line << "\n";
first=0;
}
}else
filePtr = forFile;
continue;
}
cout << line << endl;
cout << line << "\n";
}
cout << last_line << endl;
cout << last_line << "\n";
filePtr = revFile;
while(getline((*filePtr), line).good())
cout << line << endl;
cout << line << "\n";
(*revFile).close();
(*forFile).close();
......