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sci-biology/lagan: Port to EAPI 7 

* Fix building against GCC 10 / -fno-common
* Fix building against C99 / -O0
* Fix broken build system
* Import patches from Debian

Closes: https://bugs.gentoo.org/685736
Closes: https://bugs.gentoo.org/688700
Closes: https://bugs.gentoo.org/707404
Package-Manager: Portage-3.0.8, Repoman-3.0.2
Signed-off-by: David Seifert <soap@gentoo.org>
This commit is contained in:
David Seifert 2020-11-01 19:36:21 +01:00
parent 6c107298cc
commit 053ec438e9
No known key found for this signature in database
GPG Key ID: CE36E117202E3842
12 changed files with 550 additions and 664 deletions
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258
sci-biology/lagan/files/lagan-2.0-C99-static-inline.patch Normal file
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@ -0,0 +1,258 @@
--- a/src/fchaos.c
+++ b/src/fchaos.c
@@ -985,7 +985,7 @@
SLremove(mylist, tbf->mysles[i]);
}
-inline int CHmatchscore(unsigned char a, unsigned char b) {
+static inline int CHmatchscore(unsigned char a, unsigned char b) {
return substmatrix[a][b];
/*
if (translated)
--- a/src/multial.c
+++ b/src/multial.c
@@ -59,16 +59,16 @@
int normf;
int normprev;
-inline int ismatch(char a, char b) {
+static inline int ismatch(char a, char b) {
return (a == b);
}
-inline int isGap(align* ali, int seqn, int loc) {
+static inline int isGap(align* ali, int seqn, int loc) {
int i = !((ali->algn[loc] >> seqn) & 1);
return i;
}
-inline int scoreLocal(int which, align* ali, int loc) {
+static inline int scoreLocal(int which, align* ali, int loc) {
int i, lets = 0;
for (i=0; i < 4; i++)
lets += ali->cnts[i][loc];
@@ -83,7 +83,7 @@
return lets+ali->cnts[CNTS_GS][loc] * gapcont;
}
-inline hll* reverseHLL(hll* tbr) {
+static inline hll* reverseHLL(hll* tbr) {
hll *nn, *prev=0;
while (tbr) {
nn = tbr->next;
@@ -171,7 +171,7 @@
return res;
}
-inline void reverse (long long int* a, int length) {
+static inline void reverse (long long int* a, int length) {
long long int lft;
int i;
for (i=0; i < length/2; i++) {
@@ -409,7 +409,7 @@
*/
}
-inline int scoreGap(int numgs, int numgc, int numge, int numseq) {
+static inline int scoreGap(int numgs, int numgc, int numge, int numseq) {
return (MIN2(numgc, numseq-numgc) * gapcont) +
(MIN2(numgs, numseq-numgs) * gapstart) +
(MIN2(numge, numseq-numge) * gapend);
@@ -493,7 +493,7 @@
fclose (file);
}
-inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) {
+static inline int chmatchscore (unsigned char a, unsigned char b, int substmatrix[256][256]) {
return substmatrix[a][b];
}
@@ -539,14 +539,14 @@
// printcache();
}
-inline int v (int y){
+static inline int v (int y){
if (y >= 0 && y <= MAX_SEQ) return y;
fprintf(stderr, "Got %d in v\n", y);
assert (0);
return 0;
}
-inline int matchscore (align*a, int ai, align *b, int bi){
+static inline int matchscore (align*a, int ai, align *b, int bi){
return
matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) |
@@ -559,30 +559,30 @@
(v(a->numseq + b->numseq - (a->cnts[CNTS_CB][ai] + b->cnts[CNTS_CB][bi])) << 18)];
}
-inline int scoreOpp (align *other, int ow, int oppnum){
+static inline int scoreOpp (align *other, int ow, int oppnum){
return matchcache[v(other->cnts[0][ow]) |
(v(other->cnts[1][ow]) << 6) |
(v(other->cnts[2][ow]) << 12) |
(v(other->cnts[3][ow]) << 18)];
}
-inline int endGap0 (align* a, int ai, align* b, int bi){
+static inline int endGap0 (align* a, int ai, align* b, int bi){
return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) |
(v(a->numseq + b->numseq-(b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
}
-inline int endGap1 (align* a, int ai, align* b, int bi){
+static inline int endGap1 (align* a, int ai, align* b, int bi){
return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) |
(v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
}
-inline int endGap2 (align* a, int ai, align* b, int bi){
+static inline int endGap2 (align* a, int ai, align* b, int bi){
return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) |
(v(a->numseq + b->numseq - (b->cnts[CNTS_CB][bi]+a->cnts[CNTS_CB][ai])) << 18)];
}
-inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) {
+static inline int contGap(align* ali, int myw, align* other, int ow, int *sopp) {
return gapcache[(v(other->cnts[CNTS_GS][ow])) |
(v(ali->numseq + other->cnts[CNTS_GC][ow]) << 6) |
(v(other->cnts[CNTS_GE][ow]) << 12) |
@@ -590,7 +590,7 @@
sopp[ow];
}
-inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) {
+static inline int openGap(align* ali, int w, align* other, int ow, int *sopp, char *desc) {
int alopen, pen, sav, i;
alopen = ali->cnts[CNTS_GC][w] + ali->cnts[CNTS_GE][w];
--- a/src/order.c
+++ b/src/order.c
@@ -454,11 +454,11 @@
}
-inline int ismatch(char a, char b) {
+static inline int ismatch(char a, char b) {
return a == b;
}
-inline int matchscore (unsigned char a, unsigned char b) {
+static inline int matchscore (unsigned char a, unsigned char b) {
return substmatrix[a][b];
/*
--- a/src/utils/cstat.c
+++ b/src/utils/cstat.c
@@ -121,7 +121,7 @@
return res;
}
-inline int getScore (align* a, int i){
+static inline int getScore (align* a, int i){
return
((a->cnts[0][i] * (a->cnts[0][i] - 1)) +
(a->cnts[1][i] * (a->cnts[1][i] - 1)) +
--- a/src/utils/getbounds.c
+++ b/src/utils/getbounds.c
@@ -6,8 +6,8 @@
#define EXPAND 2
-inline int max (int a, int b){ if (a > b) return a; return b; }
-inline int min (int a, int b){ if (a < b) return a; return b; }
+static inline int max (int a, int b){ if (a > b) return a; return b; }
+static inline int min (int a, int b){ if (a < b) return a; return b; }
int getLength (char *filename){
FILE *file;
--- a/src/utils/scorealign.c
+++ b/src/utils/scorealign.c
@@ -18,17 +18,17 @@
int matchscore[256][256];
int gapopen = -1500, gapcont = -50;
-inline int min (int a, int b){
+static inline int min (int a, int b){
if (a < b) return a;
return b;
}
-inline int max (int a, int b){
+static inline int max (int a, int b){
if (a > b) return a;
return b;
}
-inline int scoreMatch (char c, char d){
+static inline int scoreMatch (char c, char d){
if (c == '-' && d == '-') return 0;
if (c == '-' || d == '-') return gapcont;
return matchscore[(unsigned char) c][(unsigned char) d];
@@ -235,7 +235,7 @@
}
}
-inline int issymbol (char ch){
+static inline int issymbol (char ch){
return ch == 'A' || ch == 'C' || ch == 'G' || ch == 'T' || ch == 'N' || ch == '.' || ch == '-';
}
--- a/src/utils/scorecontigs.c
+++ b/src/utils/scorecontigs.c
@@ -133,7 +133,7 @@
return res;
}
-inline int getstate (char c, char d){
+static inline int getstate (char c, char d){
if (c == '-' || d == '-') return 2;
if (c == 'N' || d == 'N') return 3;
return c == d;
@@ -235,7 +235,7 @@
return r;
}
-inline int getdata (rangelist **ranges, int *offs, int j, int i){
+static inline int getdata (rangelist **ranges, int *offs, int j, int i){
i -= offs[j];
if (i >= 0 && i < ranges[j]->seqlen)
return ranges[j]->score[i];
@@ -243,14 +243,14 @@
}
-inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){
+static inline int match (rangelist **ranges, int numContigs, int i, int j, int *offs){
int k;
for (k = 0; k < numContigs; k++)
if ((getdata (ranges, offs, k, i) != 0) != (getdata (ranges, offs, k, j) != 0)) return 0;
return 1;
}
-inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){
+static inline int allzeroes (rangelist **ranges, int numContigs, int pos, int *offs){
int i;
for (i = 0; i < numContigs; i++)
@@ -258,7 +258,7 @@
return 1;
}
-inline void print (int start, int end, int *score, int numContigs){
+static inline void print (int start, int end, int *score, int numContigs){
int j;
printf ("(%7d %7d)", start, end);
@@ -303,7 +303,7 @@
free (pattern);
}
-inline double scoregap (int gaplen){
+static inline double scoregap (int gaplen){
if (gaplen == 0) return 0;
//return (gaplen - 1) * -1 - 50;
return (log (gaplen) / log (10) + 1) * scoreGapOpen;

49
sci-biology/lagan/files/lagan-2.0-ambiguous-end.patch Normal file
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@ -0,0 +1,49 @@
Author: Steffen Moeller
Last-Update: 2018-09-07 15:08:19 +0200
Description: Fix build issue
Index: lagan/src/glocal/rightinfluence.cpp
===================================================================
--- lagan.orig/src/glocal/rightinfluence.cpp
+++ lagan/src/glocal/rightinfluence.cpp
@@ -1,6 +1,6 @@
#include <rightinfluence.h>
-Fragment origin, end;
+static Fragment originFrag, endFrag;
// Sets the first default owner of the whole region
void initRI(RI *RightInfluence, long long int scoreIndex) {
@@ -13,22 +13,22 @@ void initRI(RI *RightInfluence, long lon
}
// will lose to anyone
- origin.seq1End = 0; origin.seq2End = 0;
- origin.seq1Start = 0; origin.seq2Start = 0;
+ originFrag.seq1End = 0; originFrag.seq2End = 0;
+ originFrag.seq1Start = 0; originFrag.seq2Start = 0;
// hack to aid winner selection
- origin.score = -1;
- end.score = -2;
- origin.totalScore = end.totalScore = 0;
+ originFrag.score = -1;
+ endFrag.score = -2;
+ originFrag.totalScore = endFrag.totalScore = 0;
// will win against anyone
- end.seq1End = 0; end.seq2End = 0;
- end.seq1Start = 0; end.seq2Start = 0;
+ endFrag.seq1End = 0; endFrag.seq2End = 0;
+ endFrag.seq1Start = 0; endFrag.seq2Start = 0;
- origin.back = NULL;
+ originFrag.back = NULL;
- RightInfluence->act[-INF] = &origin;
- RightInfluence->act[+INF] = &end;
+ RightInfluence->act[-INF] = &originFrag;
+ RightInfluence->act[+INF] = &endFrag;
}

24
sci-biology/lagan/files/lagan-2.0-conflicting-getline.patch Normal file
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@ -0,0 +1,24 @@
Author: Andreas Tille <tille@debian.org>
LastChanged: Fri, 15 Nov 2013 10:31:20 +0100
Description: Prevent conflicting getline by simply renaming it
--- a/src/anchors.c
+++ b/src/anchors.c
@@ -225,7 +225,7 @@ char* rolltonum(char* str) {
return &str[i];
}
-int getline(FILE* infile, hll* tt) {
+int anchors_getline(FILE* infile, hll* tt) {
char temp[1024];
char* help;
int z, h;
@@ -248,7 +248,7 @@ hll* parseCHAOS(FILE* infile, int* totnu
*totnum = 0;
while(!feof(infile)) {
tt = (hll*) malloc(sizeof(hll));
- while (!feof(infile) && !getline(infile, tt))
+ while (!feof(infile) && !anchors_getline(infile, tt))
;
if (feof(infile)) break;
if (gapfreechunks) {

473
sci-biology/lagan/files/lagan-2.0-fix-c++14.patch
View File

@ -1,473 +0,0 @@
Fix building with C++14, which errors out due to namespace collisions with std::end
in C++14 mode, due to crappy 'using namespace std' declared everywhere.
See also: https://bugs.gentoo.org/show_bug.cgi?id=594148
--- a/src/ancseq.cpp
+++ b/src/ancseq.cpp
@@ -30,7 +30,6 @@
#include <stdlib.h>
#include <stdio.h>
-using namespace std;
#include "util.cpp"
#include "faindex.cpp"
--- a/src/ancseqrest.cpp
+++ b/src/ancseqrest.cpp
@@ -31,7 +31,6 @@
#include <stdlib.h>
#include <stdio.h>
-using namespace std;
#define fastaRowLength 50
typedef char* pchar;
--- a/src/cutmfa.cpp
+++ b/src/cutmfa.cpp
@@ -45,7 +45,6 @@
#include <stdlib.h>
#include <stdio.h>
-using namespace std;
// TODO refactor in classes and normal make project
--- a/src/glocal/glocal.cpp
+++ b/src/glocal/glocal.cpp
@@ -7,9 +7,9 @@
}
//vectors that would be needed globally
-vector<Fragment> fragments;
-vector<Point>startPoints;
-vector<Point>endPoints;
+std::vector<Fragment> fragments;
+std::vector<Point>startPoints;
+std::vector<Point>endPoints;
long long int numFragments;
InterPoint inter;
@@ -19,7 +19,7 @@
RI RI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
LI LI_regions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
-vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
+std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
Name allNames;
--- a/src/glocal/io.cpp
+++ b/src/glocal/io.cpp
@@ -3,9 +3,9 @@
#include<io.h>
#include<algorithm>
-extern vector <Fragment> fragments;
-extern vector <Point> startPoints;
-extern vector <Point> endPoints;
+extern std::vector <Fragment> fragments;
+extern std::vector <Point> startPoints;
+extern std::vector <Point> endPoints;
extern Name allNames;
bool PointCompare(const Point &f1, const Point &f2) {
@@ -223,8 +223,8 @@
startPoints.push_back(startPoint);
endPoints.push_back(endPoint);
}
- sort(startPoints.begin(), startPoints.end(), PointCompare);
- sort(endPoints.begin(), endPoints.end(), PointCompare);
+ std::sort(startPoints.begin(), startPoints.end(), PointCompare);
+ std::sort(endPoints.begin(), endPoints.end(), PointCompare);
}
--- a/src/glocal/leftinfluence.cpp
+++ b/src/glocal/leftinfluence.cpp
@@ -154,8 +154,8 @@
if (second->score == -1) { return TRUE; }
- dummy.seq1Start = max(first->seq1End, second->seq1End) + 2;
- dummy.seq2Start = max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1;
+ dummy.seq1Start = std::max(first->seq1End, second->seq1End) + 2;
+ dummy.seq2Start = std::max(first->getSeq2End(LeftInfluence->reflectFlag), second->getSeq2End(LeftInfluence->reflectFlag)) + 1;
if (first->getSeq2End(LeftInfluence->reflectFlag) > second->getSeq2End(LeftInfluence->reflectFlag)) {
dummy.nameIter = first->nameIter;
@@ -444,7 +444,7 @@
temp.seq1 = col - diag;
temp.seq2 = col;
- pair<Point,LI*> pairp(temp, LeftInfluence);
+ std::pair<Point,LI*> pairp(temp, LeftInfluence);
tempinter = inter.insert(pairp);
colInter->second = tempinter;
--- a/src/glocal/leftinfluence.h
+++ b/src/glocal/leftinfluence.h
@@ -39,15 +39,15 @@
-typedef list<Fragment*> Owner;
-typedef map <long long int ,Owner::iterator,longlongCompare2> CBound;
+typedef std::list<Fragment*> Owner;
+typedef std::map <long long int ,Owner::iterator,longlongCompare2> CBound;
-typedef multimap <Point ,struct LI *,paircomp> InterPoint;
+typedef std::multimap <Point ,struct LI *,paircomp> InterPoint;
-typedef map <long long int ,InterPoint::iterator,longlongCompare2> CInter;
-typedef map <long long int,Owner::iterator,longlongCompare2> DBound;
+typedef std::map <long long int ,InterPoint::iterator,longlongCompare2> CInter;
+typedef std::map <long long int,Owner::iterator,longlongCompare2> DBound;
-typedef map <long long int,InterPoint::iterator,longlongCompare2> DInter;
+typedef std::map <long long int,InterPoint::iterator,longlongCompare2> DInter;
--- a/src/glocal/rightinfluence.h
+++ b/src/glocal/rightinfluence.h
@@ -17,7 +17,7 @@
};
-typedef map<const long long int , Fragment*,longlongCompare> Active;
+typedef std::map<const long long int , Fragment*,longlongCompare> Active;
typedef struct RI {
//List of active regions
--- a/src/glocal/score.cpp
+++ b/src/glocal/score.cpp
@@ -4,7 +4,7 @@
#include<rightinfluence.h>
#include<fstream>
-extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
+extern std::vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
float Score::getScore(Fragment *up, Fragment * down) {
@@ -36,7 +36,7 @@
void initScoreFunctionPointers(char * scoreFileName) {
- ifstream SFP;
+ std::ifstream SFP;
char line[255];
SFP.open(scoreFileName);
--- a/src/glocal/structs.h
+++ b/src/glocal/structs.h
@@ -12,7 +12,6 @@
#include <list>
#include <string.h>
-using namespace std;
#define RIGHT 0
#define LEFT 1
@@ -49,7 +48,7 @@
};
-typedef map<const char*,long long int ,ltstr> Name;
+typedef std::map<const char*,long long int ,ltstr> Name;
typedef struct Fragment {
--- a/src/lagan2mfa.cpp
+++ b/src/lagan2mfa.cpp
@@ -6,7 +6,6 @@
#include <stdlib.h>
#include <stdio.h>
-using namespace std;
// TODO refactor in classes and normal make project
--- a/src/makecons.cpp
+++ b/src/makecons.cpp
@@ -18,7 +18,6 @@
#include <ctype.h>
#include <time.h>
-using namespace std;
#define fastaRowLength 50
#define bufSize 2000
--- a/src/utils/Glue.cpp
+++ b/src/utils/Glue.cpp
@@ -170,7 +170,7 @@
}
void printCoordinates (int seq, int begin, int end){
- cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " ";
+ std::cout << seqs[seq].getID() << ":" << getSeqCoord(seq, begin) << "-" << getSeqCoord(seq, end) << " ";
}
int printRegion (int begin, int end){
@@ -183,7 +183,7 @@
score += rescoreRegion (seqs[i], seqs[j], begin, end);
}
}
- cout << score << endl;
+ std::cout << score << std::endl;
return score;
}
@@ -223,7 +223,7 @@
}
}
- cout << "= score=" << score << endl;
+ std::cout << "= score=" << score << std::endl;
}
int countLets (SafeVector<char> &data){
@@ -355,7 +355,7 @@
FILE* outfile;
if (argc < 2 || argc > 3){
- cerr << "Usage: Glue align.mfa \n" << endl;
+ std::cerr << "Usage: Glue align.mfa \n" << std::endl;
exit (1);
}
@@ -375,7 +375,7 @@
SafeVector<int> merged1label, merged2label;
int begin1 = 1, end1 = 1;
- ifstream data (argv[1]);
+ std::ifstream data (argv[1]);
int alignNum = 0;
strand.push_back ('?'); // nothing for alignNum 0
@@ -452,7 +452,7 @@
SafeVector<char> temp1 (begin1 - 1, 'N');
SafeVector<char> temp2 (begin1 - 1, '-');
- for (int i = 0; i < min ((int) temp2.size(), CNTG_BRK_N); i++)
+ for (int i = 0; i < std::min ((int) temp2.size(), CNTG_BRK_N); i++)
temp2[i] = 'N';
merged1 = merge (temp1, merged1);
@@ -471,12 +471,12 @@
if (isalpha(merged2[j])) pos2++;
if (merged1label[j] == i){
- min1 = min (min1, pos1);
- max1 = max (max1, pos1);
+ min1 = std::min (min1, pos1);
+ max1 = std::max (max1, pos1);
}
if (merged2label[j] == i){
- min2 = min (min2, pos2);
- max2 = max (max2, pos2);
+ min2 = std::min (min2, pos2);
+ max2 = std::max (max2, pos2);
}
}
@@ -489,6 +489,6 @@
fprintf (outfile, "%d %d %d 0 0 0 0 %c 0 %d %d\n", i, min1, max1, strand[i], min2, max2);
}
- printMFA (cout, merged1, string ("first"), 60);
- printMFA (cout, merged2, string ("second"), 60);
+ printMFA (std::cout, merged1, std::string ("first"), 60);
+ printMFA (std::cout, merged2, std::string ("second"), 60);
}
--- a/src/utils/MultiSequence.h
+++ b/src/utils/MultiSequence.h
@@ -12,7 +12,6 @@
#include "Sequence.h"
#include "SafeVector.h"
-using namespace std;
class MultiSequence {
private:
@@ -54,10 +53,10 @@
// Read in all of the Sequences in an MFA file and append them to the
// existing MultiSequence object.
- void addRawFromMFA (const string& filename){
+ void addRawFromMFA (const std::string& filename){
// open up file for reading
- ifstream infile (filename.c_str());
+ std::ifstream infile (filename.c_str());
// check for error
assert (!infile.fail());
@@ -75,7 +74,7 @@
// Read in all of the Sequences in an MFA file and append them to the
// existing MultiSequence object.
- void addRawFromMFA (ifstream &infile){
+ void addRawFromMFA (std::ifstream &infile){
// check for error
assert (!infile.fail());
@@ -89,7 +88,7 @@
}
// Writes sequences to outfile in XMFA format.
- void writeToXMFA (ostream &outfile, int numColumns) const {
+ void writeToXMFA (std::ostream &outfile, int numColumns) const {
for (int i = 0; i < (int) sequences.size(); ++i){
sequences[i].writeToXMFA (outfile, numColumns);
}
--- a/src/utils/Output.h
+++ b/src/utils/Output.h
@@ -2,18 +2,18 @@
#define OUTPUT_H
// print reversed string in MFA format
-void printMFA (ostream &outfile, SafeVector<char> &data, string comment, int numColumns){
+void printMFA (std::ostream &outfile, SafeVector<char> &data, std::string comment, int numColumns){
int charsWritten = 0;
- outfile << ">" << comment << endl;
+ outfile << ">" << comment << std::endl;
for (int i = 0; i < (int) data.size(); i++){
outfile << data[i];
charsWritten++;
- if (charsWritten % numColumns == 0) outfile << endl;
+ if (charsWritten % numColumns == 0) outfile << std::endl;
}
- if (charsWritten % numColumns != 0) outfile << endl;
+ if (charsWritten % numColumns != 0) outfile << std::endl;
}
--- a/src/utils/SafeVector.h
+++ b/src/utils/SafeVector.h
@@ -10,7 +10,6 @@
#include <assert.h>
#include <vector>
-using namespace std;
// class derived from the STL std::vector
template<class TYPE>
@@ -19,9 +18,9 @@
// miscellaneous constructors
SafeVector () {}
- SafeVector (size_t size) : vector<TYPE>(size) {}
- SafeVector (size_t size, const TYPE &value) : vector<TYPE>(size, value) {}
- SafeVector (const SafeVector &source) : vector<TYPE>(source) {}
+ SafeVector (size_t size) : std::vector<TYPE>(size) {}
+ SafeVector (size_t size, const TYPE &value) : std::vector<TYPE>(size, value) {}
+ SafeVector (const SafeVector &source) : std::vector<TYPE>(source) {}
#ifdef ENABLE_CHECKS
--- a/src/utils/Sequence.h
+++ b/src/utils/Sequence.h
@@ -8,15 +8,14 @@
#include <string>
#include "SafeVector.h"
-using namespace std;
class Sequence {
private:
// Read header of MFA/XMFA file.
- bool readHeader (ifstream &infile, bool &isXMFA){
- string header;
+ bool readHeader (std::ifstream &infile, bool &isXMFA){
+ std::string header;
while (true){
@@ -24,7 +23,7 @@
if (infile.fail() || infile.eof()) return false;
// get new header line
- getline (infile, header);
+ std::getline (infile, header);
// check that header line is not empty
if (header.length() != 0) break;
@@ -64,7 +63,7 @@
int startCoord; // sequence position of first character
int endCoord; // sequence position of last character
char direction; // + or -
- string comment; // comments
+ std::string comment; // comments
public:
@@ -77,7 +76,7 @@
}
// Constructor. Reads in a sequence from the input file.
- Sequence (ifstream &infile){
+ Sequence (std::ifstream &infile){
bool isXMFA = true;
@@ -147,7 +146,7 @@
}
// Constructor. Gets sequence from array data.
- Sequence (SafeVector<char> data, string comment) : data(data), comment(comment) {
+ Sequence (SafeVector<char> data, std::string comment) : data(data), comment(comment) {
length = data.size() - 1;
id = 0;
startCoord = 1;
@@ -165,7 +164,7 @@
return temp;
}
- const string getComment () const {
+ const std::string getComment () const {
return comment;
}
@@ -197,9 +196,9 @@
const int getEndCoord () const { assert (isValid); return endCoord; }
// Print XMFA header only.
- void writeXMFAHeader (ostream &outfile) const {
+ void writeXMFAHeader (std::ostream &outfile) const {
assert (isValid);
- outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl;
+ outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << std::endl;
}
// Return sequence ID.
@@ -209,20 +208,20 @@
void setID (int id) { assert (isValid); this->id = id; }
// Writes sequence to XMFA format.
- void writeToXMFA (ostream &outfile, int numColumns) const {
+ void writeToXMFA (std::ostream &outfile, int numColumns) const {
assert (isValid);
// print XMFA header
- outfile << ">" << comment << endl;
+ outfile << ">" << comment << std::endl;
// outfile << '>' << id << ':' << startCoord << '-' << endCoord << ' ' << direction << ' ' << comment << endl;
// print character data
for (int i = 1; i <= length; ++i){
outfile << data[i];
- if (i % numColumns == 0) outfile << endl;
+ if (i % numColumns == 0) outfile << std::endl;
}
- if (length % numColumns != 0) outfile << endl;
+ if (length % numColumns != 0) outfile << std::endl;
}
};

27
sci-biology/lagan/files/lagan-2.0-gcc-10.patch Normal file
View File

@ -0,0 +1,27 @@
Description: Add patch to build with GCC-10
Bug-Debian: https://bugs.debian.org/957415
Author: Nilesh Patra <npatra974@gmail.com>
Date: Fri Apr 17 21:13:21 2020 +0530
--- a/src/fchaos.c
+++ b/src/fchaos.c
@@ -29,7 +29,7 @@
int offset;
} match;
-extern int indeces[256];
+int indeces[256];
void remElem(LList* tbf, int i);
--- a/src/thrtrie.h
+++ b/src/thrtrie.h
@@ -2,7 +2,7 @@
#define MAX_DEGEN 2
-int indeces[256];
+extern int indeces[256];
typedef struct PrevHits {
int* inds1;

25
sci-biology/lagan/files/lagan-2.0-gcc-4.8.patch Normal file
View File

@ -0,0 +1,25 @@
Author: Andreas Tille <tille@debian.org>
LastChanged: Fri, 15 Nov 2013 10:31:20 +0100
Description: Fix some includes to build using gcc-4.8
--- a/src/utils/Glue.cpp
+++ b/src/utils/Glue.cpp
@@ -6,6 +6,7 @@
#include <fstream>
#include <iostream>
#include <algorithm>
+#include <string.h>
#define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
#define MAX_LINE_LENGTH 1024
--- a/src/glocal/score.cpp
+++ b/src/glocal/score.cpp
@@ -2,7 +2,7 @@
#include<score.h>
#include<leftinfluence.h>
#include<rightinfluence.h>
-#include<fstream.h>
+#include<fstream>
extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];

25
sci-biology/lagan/files/lagan-2.0-gcc-9.patch Normal file
View File

@ -0,0 +1,25 @@
# Two patches to bring lagan up to speed with gcc-9
Index: lagan/src/fchaos.c
===================================================================
--- lagan.orig/src/fchaos.c
+++ lagan/src/fchaos.c
@@ -430,7 +430,7 @@ int chain(LList* second, int off2, LList
int tc =0;
int wc = 0;
-inline void findPrev(LList* curr, int position, int offset, float baseval) {
+void findPrev(LList* curr, int position, int offset, float baseval) {
int j,k;
LList* temp;
sle* iterator;
Index: lagan/src/filebuffer.c
===================================================================
--- lagan.orig/src/filebuffer.c
+++ lagan/src/filebuffer.c
@@ -1,5 +1,6 @@
#include "filebuffer.h"
#include <stdlib.h>
+#include <ctype.h>
#include <string.h>
#include <stdio.h>
#include <assert.h>

23
sci-biology/lagan/files/lagan-2.0-gcc4.3.patch
View File

@ -1,23 +0,0 @@
diff -durr lagan20-orig/src/glocal/score.cpp lagan20/src/glocal/score.cpp
--- lagan20-orig/src/glocal/score.cpp 2009-02-04 15:25:57.698333297 +0000
+++ lagan20/src/glocal/score.cpp 2009-02-04 15:27:23.894092890 +0000
@@ -2,7 +2,7 @@
#include<score.h>
#include<leftinfluence.h>
#include<rightinfluence.h>
-#include<fstream.h>
+#include<fstream>
extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
diff -durr lagan20-orig/src/utils/Glue.cpp lagan20/src/utils/Glue.cpp
--- lagan20-orig/src/utils/Glue.cpp 2009-02-04 15:25:57.702333182 +0000
+++ lagan20/src/utils/Glue.cpp 2009-02-04 15:27:04.190822654 +0000
@@ -1,6 +1,7 @@
#include "MultiSequence.h"
#include "SafeVector.h"
#include "Output.h"
+#include <string.h>
#include <math.h>
#include <assert.h>
#include <fstream>

109
sci-biology/lagan/files/lagan-2.0-flags.patch → sci-biology/lagan/files/lagan-2.0-makefile.patch
View File

@ -1,107 +1,120 @@
diff --git a/Makefile b/Makefile
index fbbbe79..a1d449b 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
@@ -1,5 +1,8 @@
all:
- (cd src; $(MAKE))
+ $(MAKE) -C src
clean:
rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
(cd src; $(MAKE) clean)
diff --git a/src/Makefile b/src/Makefile
index 7f6b6fd..dd6309b 100644
- (cd src; $(MAKE) clean)
+ $(MAKE) -C src clean
+
+check: all
+ (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]"
--- a/src/glocal/Makefile
+++ b/src/glocal/Makefile
@@ -1,19 +1,13 @@
-CC = g++
-OPTFLAGS =
-CFLAGS = $(OPTFLAGS) -O3
-CLINKER = g++
-# LIBDIR = -L/usr/local/lib
+CXXFLAGS += -Wno-deprecated
+CPPFLAGS += -I./
+
MLIB = -lm
-INCDIR = -I./
TRGT_DIR = ../..
TRGT = glocal
OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
-.cpp.o:
- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
-
$(TRGT): $(OBJECTS)
- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
clean :
rm -f *.o ./*~ *~ core
--- a/src/Makefile
+++ b/src/Makefile
@@ -4,51 +4,51 @@ CFLAGS = -O3 # -Wall -W
@@ -1,54 +1,51 @@
-CC = gcc $(CFLAGS)
-CPP = g++ $(CFLAGS)
-CFLAGS = -O3 # -Wall -W
TRGT_DIR = ..
all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
- (cd glocal; $(MAKE))
+ $(MAKE) -C glocal
+ (cd glocal && $(MAKE))
clean:
rm -f *.o *~ utils/*~ mlagan.purify core
(cd glocal; $(MAKE) clean)
- (cd glocal; $(MAKE) clean)
+ (cd glocal && $(MAKE) clean)
../anchors: anchors.c skiplist.c
- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
../order: order.c diagmatrix.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
../utils/bin2mf: utils/bin2mf.c
- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
../utils/bin2bl: utils/bin2bl.c
- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
../utils/cextract: utils/cextract.c
- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
../utils/cstat: utils/cstat.c
- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
../utils/contigorder: utils/contigorder.c
- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
../utils/getbounds: utils/getbounds.c
- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
../utils/getcontigpos: utils/getcontigpos.c
- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
../utils/getlength: utils/getlength.c
- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
../utils/getoverlap: utils/getoverlap.c
- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
../utils/rc: utils/rc.c
- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/rc utils/rc.c
../utils/seqmerge: utils/seqmerge.c
- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
../utils/scorealign: utils/scorealign.c
- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
../utils/scorecontigs: utils/scorecontigs.c
- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
../utils/fa2xfa: utils/fa2xfa.c
- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
../utils/overlay: utils/overlay.c
- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
../utils/Glue: utils/Glue.cpp
- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
../utils/dotplot: utils/dotplot.cpp
- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
diff --git a/src/glocal/Makefile b/src/glocal/Makefile
index ce1421a..b82507f 100755
--- a/src/glocal/Makefile
+++ b/src/glocal/Makefile
@@ -10,10 +10,10 @@ TRGT = glocal
OBJECTS = glocal.o io.o rightinfluence.o leftinfluence.o score.o
.cpp.o:
- $(CC) -Wno-deprecated $(CFLAGS) $(INCDIR) -c $*.cpp
+ $(CXX) $(CXXFLAGS) $(INCDIR) -c $*.cpp
$(TRGT): $(OBJECTS)
- $(CLINKER) $(OPTFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
+ $(CXX) $(LDFLAGS) $(OBJECTS) -o $(TRGT_DIR)/$(TRGT) $(MLIB)
clean :
rm -f *.o ./*~ *~ core
+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp

63
sci-biology/lagan/files/lagan-2.0-qa-implicit-declarations.patch
View File

@ -1,69 +1,34 @@
Fix QA warnings due to implicit declarations:
* filebuffer.c:123:34: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration]
* temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ?
--- a/src/filebuffer.c
+++ b/src/filebuffer.c
@@ -3,6 +3,7 @@
#include <string.h>
#include <stdio.h>
#include <assert.h>
+#include <ctype.h>
#ifdef CHAOS__FLAG
char* alphabet = "ATCGNPCMHDEKRQSILVFYWX*";
--- a/src/mlagan.c
+++ b/src/mlagan.c
@@ -934,6 +934,7 @@
return k;
@@ -46,6 +46,7 @@
return 1;
}
+int printXMFAAlign(FILE* outfile, align* myalign);
int main(int argc, char** argv) {
FileBuffer seqfile;
void usage(void) {
printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n",
--- a/src/order.c
+++ b/src/order.c
@@ -398,6 +398,9 @@
free(ends);
}
@@ -28,6 +28,8 @@
align* makeAlign(dmat* mydm, char* seq1, char* seq2);
+int printMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2);
+int printXMFAAlign(char* seq1, char* seq2, align* myalign, char* n1, char* n2);
+
void doAlign(dmat* mydm, seq* seq1, seq* seq2) {
align *a = (align*) makeAlign(mydm, seq1->lets, seq2->lets);
// printf("into printing\n");
char* alpha = "ATCGN.";
--- a/src/prolagan.c
+++ b/src/prolagan.c
@@ -949,6 +949,7 @@
return k;
@@ -49,6 +49,7 @@
return 1;
}
+int printXMFAAlign(FILE* outfile, align* myalign);
int main(int argc, char** argv) {
FileBuffer seqfile;
--- a/src/utils/contigorder.c
+++ b/src/utils/contigorder.c
@@ -12,7 +12,7 @@
int dummy, i;
if (!(file = fopen (filename, "r"))){
- fprintf (stderr, "contigorder: Error opening file: %s\n");
+ fprintf (stderr, "contigorder: Error opening file: %s\n", filename);
exit (1);
}
@@ -49,7 +49,7 @@
}
if (!(file = fopen (filename, "r"))){
- fprintf (stderr, "contigorder: Error opening file: %s\n");
+ fprintf (stderr, "contigorder: Error opening file: %s\n", filename);
exit (1);
}
void usage(void) {
printf("mlagan seqfile_1 seqfile_2 [... seqfile_%d] [-parameters]\n\n",
--- a/src/utils/cstat.c
+++ b/src/utils/cstat.c
@@ -3,6 +3,7 @@

71
sci-biology/lagan/lagan-2.0-r3.ebuild
View File

@ -1,71 +0,0 @@
# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit toolchain-funcs
MY_P="lagan20"
DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA"
HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
RDEPEND="dev-lang/perl"
S="${WORKDIR}/${MY_P}"
PATCHES=(
"${FILESDIR}/${PN}-2.0-flags.patch"
"${FILESDIR}/${PN}-2.0-gcc4.3.patch"
"${FILESDIR}/${PN}-2.0-fix-c++14.patch"
"${FILESDIR}/${PN}-2.0-qa-implicit-declarations.patch"
)
src_prepare() {
sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/${PN}/lib\";" "${S}/supermap.pl" || die
# NB: Testing with glibc-2.10 has uncovered a bug in src/utils/Sequence.h
# where libc getline is erroneously used instead of own getline
sed -i 's/getline/my_getline/' "${S}"/src/{anchors.c,glocal/io.cpp} || die
default
}
src_compile() {
emake \
CC=$(tc-getCC) \
CXX=$(tc-getCXX) \
CXXFLAGS="${CXXFLAGS}" \
CFLAGS="${CFLAGS}"
}
src_install() {
newbin lagan.pl lagan
newbin slagan.pl slagan
dobin mlagan
rm -f lagan.pl slagan.pl utils/Utils.pm || die
insinto /usr/$(get_libdir)/${PN}/lib
doins Utils.pm
exeinto /usr/$(get_libdir)/${PN}/utils
doexe utils/*
exeinto /usr/$(get_libdir)/${PN}
doexe *.pl anchors chaos glocal order prolagan
insinto /usr/$(get_libdir)/${PN}
doins *.txt
dosym /usr/$(get_libdir)/${PN}/supermap.pl /usr/bin/supermap
echo "LAGAN_DIR=\"/usr/$(get_libdir)/${PN}\"" > 99${PN} || die
doenvd 99${PN}
dodoc Readmes/README.*
}

67
sci-biology/lagan/lagan-2.0-r4.ebuild Normal file
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# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit toolchain-funcs
MY_P="lagan20"
DESCRIPTION="The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA"
HOMEPAGE="http://lagan.stanford.edu/lagan_web/index.shtml"
SRC_URI="http://lagan.stanford.edu/lagan_web/${MY_P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="dev-lang/perl"
S="${WORKDIR}/${MY_P}"
PATCHES=(
"${FILESDIR}"/${P}-makefile.patch
"${FILESDIR}"/${P}-conflicting-getline.patch
"${FILESDIR}"/${P}-gcc-4.8.patch
"${FILESDIR}"/${P}-ambiguous-end.patch
"${FILESDIR}"/${P}-gcc-9.patch
"${FILESDIR}"/${P}-gcc-10.patch
"${FILESDIR}"/${P}-C99-static-inline.patch
"${FILESDIR}"/${P}-qa-implicit-declarations.patch
)
src_prepare() {
default
sed -i "/use Getopt::Long;/ i use lib \"/usr/$(get_libdir)/lagan/lib\";" \
supermap.pl || die
}
src_configure() {
tc-export CC CXX
}
src_install() {
newbin lagan.pl lagan
newbin slagan.pl slagan
dobin mlagan
rm lagan.pl slagan.pl utils/Utils.pm || die
insinto /usr/$(get_libdir)/lagan/lib
doins Utils.pm
exeinto /usr/$(get_libdir)/lagan/utils
doexe utils/*
exeinto /usr/$(get_libdir)/lagan
doexe *.pl anchors chaos glocal order prolagan
insinto /usr/$(get_libdir)/lagan
doins *.txt
dosym ../$(get_libdir)/lagan/supermap.pl /usr/bin/supermap
newenvd - 99lagan <<- _EOF_
LAGAN_DIR="${EPREFIX}/usr/$(get_libdir)/lagan"
_EOF_
dodoc Readmes/README.*
}