1
我对使用一些外部的C库C++程序的工作。据我所知，这不是问题的原因，问题出在我的C++代码上。该程序运行良好，没有任何错误或测试数据集上的任何错误，但经过几乎整个完整的数据集后，我得到了段错误。运行GDB给了我这个段错误：C++赛格故障问题
(gdb) run -speciesMain=allMis1 -speciesOther=anoCar2 -speciesMain=allMis1 -speciesOther=anoCar2 /hive/data/genomes/allMis1/bed/lastz.anoCar2/mafRBestNet/*.maf.gz Starting program: /cluster/home/jstjohn/bin/mafPairwiseSyntenyDecay -speciesMain=allMis1 -speciesOther=anoCar2 -speciesMain=allMis1 -speciesOther=anoCar2 /hive/data/genome s/allMis1/bed/lastz.anoCar2/mafRBestNet/*.maf.gz Detaching after fork from child process 3718. Program received signal SIGSEGV, Segmentation fault. 0x0000003009cb7672 in __gnu_cxx::__exchange_and_add(int volatile*, int)() from /usr/lib64/libstdc++.so.6 (gdb) up #1 0x0000003009c9db59 in std::basic_string, std::allocator >::~basic_string()() from /usr/lib64/libstdc++.so.6 (gdb) up #2 0x00000000004051e7 in PairAlnInfo::~PairAlnInfo (this=0x7fffffffcd70, __in_chrg=) at mafPairwiseSyntenyDecay.cpp:37 (gdb) up #3 0x0000000000404eb0 in main (argc=2, argv=0x7fffffffcf78) at mafPairwiseSyntenyDecay.cpp:260
它看上去就像是怎么回事了双自由我PairAlnInfo类的。奇怪的是我没有定义析构函数，我也没有用new来分配任何东西。我已经在linux机器上用g ++ 44和g ++ 4.1.2尝试了这一点，并得到了相同的结果。为了使事情变得更加奇特，在我的Linux机器上（有更多可用的RAM和一切，不是RAM是这个程序的问题，但它是一个强大的系统），在程序到达之前，seg故障发生如上所述循环打印输出。在使用或者G ++或铛++我小很多的MacBook Air，该程序仍出现segfaults，但它没有做到这一点，直到后结果打印，最后return(0)出来的主要功能之前。下面是GDB跟踪的样子与Mac的默认G ++ 4.2编译后在同一个文件上运行我的Mac：
(more results)... 98000 27527 162181 0.83027 99000 27457 161467 0.829953 100000 27411 160794 0.829527 Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x00004a2c00106077 0x00007fff9365a6e5 in std::string::_Rep::_M_dispose() (gdb) up #1 0x00007fff9365a740 in std::basic_string, std::allocator >::~basic_string() (gdb) up #2 0x0000000100003938 in main (argc=1261, argv=0x851d5fbff533) at mafPairwiseSyntenyDecay.cpp:301 (gdb)
万一你没有注意到我的帖子的时候，它是关于2 ：现在30AM ...我现在已经在这个问题上砍了10个小时了。非常感谢您抽出宝贵时间看看并帮助我！下面是代码和一些复制我的情况的说明。
如果你有兴趣下载与安装依赖整个事情然后下载我KentLib库，make在基本目录，然后去examples/mafPairwiseSyntenyDecay和运行make那里。导致我讨论这个bug的一个例子（相当大）是这里提供的gziped文件：100Mb file that the program crashes on。然后用这些参数执行程序-speciesMain=allMis1 -speciesOther=anoCar2 anoCar2.allMis1.rbest.maf.gz。
/**
* mafPairwiseSyntenyDecay
* Author: John St. John
* Date: 4/26/2012
*
* calculates the mean synteny decay in different range bins
*
*
*/
//Kent source C imports
extern "C" {
#include "common.h"
#include "options.h"
#include "maf.h"
}
#include <map>
#include <string>
#include <set>
#include <vector>
#include <sstream>
#include <iostream>
//#define NDEBUG
#include <assert.h>
using namespace std;
/*
Global variables
*/
class PairAlnInfo {
public:
string oname;
int sstart;
int send;
int ostart;
int oend;
char strand;
PairAlnInfo(string _oname,
int _sstart, int _send,
int _ostart, int _oend,
char _strand):
oname(_oname),
sstart(_sstart),
send(_send),
ostart(_ostart),
oend(_oend),
strand(_strand){}
PairAlnInfo():
oname("DUMMY"),
sstart(-1),
send(-1),
ostart(-1),
oend(-1),
strand(-1){}
};
vector<string> &split(const string &s, char delim, vector<string> &elems) {
stringstream ss(s);
string item;
while(getline(ss, item, delim)) {
elems.push_back(item);
}
return(elems);
}
vector<string> split(const string &s, char delim) {
vector<string> elems;
return(split(s, delim, elems));
}
#define DEF_MIN_LEN (200)
#define DEF_MIN_SCORE (200)
typedef map<int,PairAlnInfo> PairAlnInfoByPos;
typedef map<string, PairAlnInfoByPos > ChromToPairAlnInfoByPos;
ChromToPairAlnInfoByPos pairAlnInfoByPosByChrom;
void usage()
/* Explain usage and exit. */
{
errAbort(
(char*)"mafPairwiseSyntenyDecay -- Calculates pairwise syntenic decay from maf alignment containing at least the two specified species.\n"
"usage:\n"
"\tmafPairwiseSyntenyDecay [options] [*required options] file1.maf[.gz] ... \n"
"Options:\n"
"\t-help\tPrints this message.\n"
"\t-minScore=NUM\tMinimum MAF alignment score to consider (default 200)\n"
"\t-minAlnLen=NUM\tMinimum MAF alignment block length to consider (default 200)\n"
"\t-speciesMain=NAME\t*Name of the main species (exactly as it appears before the '.') in the maf file (REQUIRED)\n"
"\t-speciesOther=NAME\t*Name of the other species (exactly as it appears before the '.') in the maf file (REQUIRED)\n"
);
}//end usage()
static struct optionSpec options[] = {
/* Structure holding command line options */
{(char*)"help",OPTION_STRING},
{(char*)"minScore",OPTION_INT},
{(char*)"minAlnLen",OPTION_INT},
{(char*)"speciesMain",OPTION_STRING},
{(char*)"speciesOther",OPTION_STRING},
{NULL, 0}
}; //end options()
/**
* Main function, takes filenames for paired qseq reads
* and outputs three files.
*/
int iterateOverAlignmentBlocksAndStorePairInfo(char *fileName, const int minScore, const int minAlnLen, const string speciesMain, const string speciesOther){
struct mafFile * mFile = mafOpen(fileName);
struct mafAli * mAli;
//loop over alignment blocks
while((mAli = mafNext(mFile)) != NULL){
struct mafComp *first = mAli->components;
int seqlen = mAli->textSize;
//First find and store set of duplicates in this block
set<string> seen;
set<string> dups;
if(mAli->score < minScore || seqlen < minAlnLen){
//free here and pre-maturely end
mafAliFree(&mAli);
continue;
}
for(struct mafComp *item = first; item != NULL; item = item->next){
string tmp(item->src);
string tname = split(tmp,'.')[0];
if(seen.count(tname)){
//seen this item
dups.insert(tname);
}else{
seen.insert(tname);
}
}
for(struct mafComp *item1 = first; item1->next != NULL; item1 = item1->next){
//stop one before the end
string tmp1(item1->src);
vector<string> nameSplit1(split(tmp1,'.'));
string name1(nameSplit1[0]);
if(dups.count(name1) || (name1 != speciesMain && name1 != speciesOther)){
continue;
}
for(struct mafComp *item2 = item1->next; item2 != NULL; item2 = item2->next){
string tmp2(item2->src);
vector<string> nameSplit2(split(tmp2,'.'));
string name2 = nameSplit2[0];
if(dups.count(name2) || (name2 != speciesMain && name2 != speciesOther)){
continue;
}
string chr1(nameSplit1[1]);
string chr2(nameSplit2[1]);
char strand;
if(item1->strand == item2->strand)
strand = '+';
else
strand = '-';
int start1,end1,start2,end2;
if(item1->strand == '+'){
start1 = item1->start;
end1 = start1 + item1->size;
}else{
end1 = item1->start;
start1 = end1 - item1->size;
}
if(item2->strand == '+'){
start2 = item2->start;
end2 = start2+ item2->size;
}else{
end2 = item2->start;
start2 = end2 - item2->size;
}
if(name1 == speciesMain){
PairAlnInfo aln(chr2,start1,end1,start2,end2,strand);
pairAlnInfoByPosByChrom[chr1][start1] = aln;
}else{
PairAlnInfo aln(chr1,start2,end2,start1,end1,strand);
pairAlnInfoByPosByChrom[chr2][start2] = aln;
}
} //end loop over item2
} //end loop over item1
mafAliFree(&mAli);
}//end loop over alignment blocks
mafFileFree(&mFile);
return(0);
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if(optionExists((char*)"help") || argc <= 1){
usage();
}
int minAlnScore = optionInt((char*)"minScore",DEF_MIN_SCORE);
int minAlnLen = optionInt((char*)"minAlnLen",DEF_MIN_LEN);
string speciesMain(optionVal((char*)"speciesMain",NULL));
string speciesOther(optionVal((char*)"speciesOther",NULL));
if(speciesMain.empty() || speciesOther.empty())
usage();
//load the relevant alignment info from the maf(s)
for(int i = 1; i<argc; i++){
iterateOverAlignmentBlocksAndStorePairInfo(argv[i], minAlnScore, minAlnLen, speciesMain, speciesOther);
}
const int blockSize = 1000;
const int blockCount = 100;
int totalWindows[blockCount] = {0};
int containBreak[blockCount] = {0};
//we want the fraction of windows of each size that contain a break
//
for(ChromToPairAlnInfoByPos::iterator mainChromItter = pairAlnInfoByPosByChrom.begin();
mainChromItter != pairAlnInfoByPosByChrom.end();
mainChromItter++){
//process the alignments shared by this chromosome
//note that map stores them sorted by begin position
vector<int> keys;
for(PairAlnInfoByPos::iterator posIter = mainChromItter->second.begin();
posIter != mainChromItter->second.end();
posIter++){
keys.push_back(posIter->first);
}
for(int i = 0; i < keys.size(); i++){
//first check for trivial window (ie our block)
PairAlnInfo pi1 = mainChromItter->second[keys[i]];
assert(pi1.send > pi1.sstart);
assert(pi1.sstart == keys[i]);
int numBucketsThisWindow = (pi1.send - pi1.sstart)/blockSize;
for(int k = 0; k < numBucketsThisWindow && k < blockCount; k++)
totalWindows[k]++;
for(int j = i+1; j < keys.size(); j++){
PairAlnInfo pi2 = mainChromItter->second[keys[j]];
assert(pi2.sstart == keys[j]);
assert(pi2.send > pi2.sstart);
assert(pi2.sstart > pi1.sstart);
if(pi2.oname == pi1.oname){
int moreToInc = (pi2.send - pi1.sstart)/blockSize;
for(int k = numBucketsThisWindow; k < moreToInc && k < blockCount; k++)
totalWindows[k]++;
numBucketsThisWindow = moreToInc; //so we don't double count
}else{
int numDiscontigBuckets = (pi2.send - pi1.sstart)/blockSize;
for(int k = numBucketsThisWindow; k < numDiscontigBuckets && k < blockSize; k++){
containBreak[k]++;
totalWindows[k]++;
}
numBucketsThisWindow = numDiscontigBuckets;
}
if((keys[j] - keys[i]) >= (blockSize * blockCount)){
//i = j;
break;
}
}
}
}
cout << "#WindowSize\tNumContainBreak\tNumTotal\t1-(NumContainBreak/NumTotal)" << endl;
for(int i = 0; i < blockCount; i++){
cout << (i+1)*blockSize << '\t';
cout << containBreak[i] << '\t';
cout << totalWindows[i] << '\t';
cout << (totalWindows[i] > 0? 1.0 - (double(containBreak[i])/double(totalWindows[i])): 0) << endl;
}
return(0);
} //end main()
肯定看起来像堆在程序的某个地方覆盖。可能来自超出范围的访问，通过查看源代码很难找到。 – 2012-04-28 09:53:03