rcanovas
commented
13 years ago Hi I don't know what could it be, but I will try to fixed as soon as I can. Anyway if you want to discuss about the implementation, most of the time I'm in room 4.31a in the 4th floor of the ICT building.
Best, Rodrigo
On Mon, Aug 1, 2011 at 9:13 PM, skuruppu < reply@reply.github.com>wrote:
I was attempting to construct a compressed suffix tree for this DNA sequence.
The suffix array is constructed successfully (at least I think so) but as soon as you invoke any methods that requires traversing the tree, a segmentation fault occurs. For example, invoking the following method call
cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);
where node_vl and node_vr are obtained from cst->Root(), causes a segmentation fault.
The following methods were invoked to construct the suffix tree.
SuffixTree *cst; SuffixTreeY csty(text, length, DAC, CN_NPR, 32); cst = &csty;
The stack trace from gdb is as follows:
0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820, len=6,
index=65836) at ../includes/libcdsTrees.h:26
1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0, x=1,
y=11309, r=1, min_r=0x7fffa70200e0) at static/suffixtree/NPR_CN.cpp:413
2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0, x=1,
y=361925, r=0, min_r=0x7fffa7020198) at static/suffixtree/NPR_CN.cpp:408
3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0, x=1,
y=11581659, csa=0xfe2a60, lcp=0xfc76b0) at static/suffixtree/NPR_CN.cpp:348
4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth (this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
5 0x0000000000404eba in cds_static::SuffixTreeY::Child (this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308, child_r=0x7fffa7020300) at static/suffixtree/SuffixTreeY.cpp:279
6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698) at
testSuffixTree.cpp:92
Hope this is enough information to fix the problem.
Reply to this email directly or view it on GitHub: https://github.com/fclaude/libcds/issues/1
skuruppu
I was attempting to construct a compressed suffix tree for this DNA sequence.
The suffix array is constructed successfully (at least I think so) but as soon as you invoke any methods that requires traversing the tree, a segmentation fault occurs. For example, invoking the following method call
where node_vl and node_vr are obtained from cst->Root(), causes a segmentation fault.
The following methods were invoked to construct the suffix tree.
The stack trace from gdb is as follows:
0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820, len=6, index=65836) at ../includes/libcdsTrees.h:26
1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0, x=1, y=11309, r=1, min_r=0x7fffa70200e0)
2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0, x=1, y=361925, r=0, min_r=0x7fffa7020198)
3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0, x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth (this=0xfc7680, vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
5 0x0000000000404eba in cds_static::SuffixTreeY::Child (this=0xfc7680, vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at testSuffixTree.cpp:52
7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698) at testSuffixTree.cpp:92
Hope this is enough information to fix the problem.