From: Andrei Zavada <johnhom...@gmail.com>
---
MUMmer3.20/src/tigr/delta2blocks.cc | 5 +----
MUMmer3.20/src/tigr/repeat-match.cc | 4 ++--
MUMmer3.20/src/tigr/show-aligns.cc | 3 +--
.../library/seqan/graph_msa/graph_align_tcoffee_io.h | 16 ++++++++--------
.../graph_algorithm_refine_exact_iterative.h | 20 ++++++++++----------
5 files changed, 22 insertions(+), 26 deletions(-)
diff --git a/MUMmer3.20/src/tigr/delta2blocks.cc
b/MUMmer3.20/src/tigr/delta2blocks.cc
index 13d8c83..982a428 100644
--- a/MUMmer3.20/src/tigr/delta2blocks.cc
+++ b/MUMmer3.20/src/tigr/delta2blocks.cc
@@ -121,8 +121,6 @@ long int revC
int main
(int argc, char ** argv)
{
- long int i;
-
FILE * RefFile = NULL;
FILE * QryFile = NULL;
@@ -368,7 +366,7 @@ void printAlignments
int Sign;
long int Delta;
- long int Total, Errors, Remain;
+ long int Total, Remain;
long int sR, eR, sQ, eQ;
long int Apos, Bpos;
@@ -441,7 +439,6 @@ void printAlignments
Apos = sR;
Bpos = sQ;
- Errors = 0;
Total = 0;
Remain = eR - sR + 1;
diff --git a/MUMmer3.20/src/tigr/repeat-match.cc
b/MUMmer3.20/src/tigr/repeat-match.cc
index 0ee308b..a4bf103 100644
--- a/MUMmer3.20/src/tigr/repeat-match.cc
+++ b/MUMmer3.20/src/tigr/repeat-match.cc
@@ -1266,14 +1266,14 @@ void Set_Subtree_Size
// string-depth in the suffix tree.
{
- int Start, Depth;
+ int Depth;
if (Root == NIL)
return;
if (Is_Leaf)
{
- Start = Leaf_Array [Root] . Lo - Parent_Depth;
+ //Start = Leaf_Array [Root] . Lo - Parent_Depth;
if (Leaf_Array [Root] . Is_Duplicate)
Node_Array [Parent] . Subtree_Size ++;
else
diff --git a/MUMmer3.20/src/tigr/show-aligns.cc
b/MUMmer3.20/src/tigr/show-aligns.cc
index a87944b..923a65c 100644
--- a/MUMmer3.20/src/tigr/show-aligns.cc
+++ b/MUMmer3.20/src/tigr/show-aligns.cc
@@ -338,7 +338,7 @@ void printAlignments
int Sign;
long int Delta;
- long int Total, Errors, Remain;
+ long int Total, Remain;
long int Pos;
long int sR, eR, sQ, eQ;
@@ -434,7 +434,6 @@ void printAlignments
Apos = sR;
Bpos = sQ;
- Errors = 0;
Total = 0;
Remain = eR - sR + 1;
diff --git
a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_io.h
b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_io.h
index 2152046..0741c98 100644
--- a/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_io.h
+++ b/mugsy-seqan/projects/library/seqan/graph_msa/graph_align_tcoffee_io.h
@@ -1046,20 +1046,20 @@ read(TFile & file,
typedef typename Iterator<TAlignmentString,Standard>::Type
TAliIterator;
TAliIterator ali_it = begin(matches,Standard())+ali_counter;
TAliIterator ali_end = end(matches,Standard());
- unsigned int seq_i_id,begin_,end_;
+ //unsigned int seq_i_id;
while(ali_it != ali_end)
{
- Fragment<> segment = *ali_it;
- seq_i_id = sequenceId(segment,0);
- begin_ = fragmentBegin(segment,seq_i_id);
- end_ = begin_ + fragmentLength(segment,seq_i_id);
+ // Fragment<> segment = *ali_it;
+ // seq_i_id = sequenceId(segment,0);
+ // begin_ = fragmentBegin(segment,seq_i_id);
+ // end_ = begin_ + fragmentLength(segment,seq_i_id);
assert(seq_i_id==seq1);
assert(seq_i_id==idToPosition(strSet,seq_i_id));
- seq_i_id = sequenceId(segment,1);
- begin_ = fragmentBegin(segment,seq_i_id);
- end_ = begin_ + fragmentLength(segment,seq_i_id);
+ // seq_i_id = sequenceId(segment,1);
+ // begin_ = fragmentBegin(segment,seq_i_id);
+ // end_ = begin_ + fragmentLength(segment,seq_i_id);
assert(seq_i_id==seq2);
assert(seq_i_id==idToPosition(strSet,seq_i_id));
diff --git
a/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_exact_iterative.h
b/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_exact_iterative.h
index d829f3d..751bfe8 100644
---
a/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_exact_iterative.h
+++
b/mugsy-seqan/projects/library/seqan/refinement/graph_algorithm_refine_exact_iterative.h
@@ -188,9 +188,9 @@ SEQAN_CHECKPOINT
// typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
//std::cout <<"create interval trees..." <<std::flush;
- clock_t start, finish1;
- double duration;
- start = clock();
+ // clock_t start, finish1;
+ //double duration;
+ // start = clock();
//one tree for each sequence
resize(gs,numSequences);
resize(pms,numSequences);
@@ -216,8 +216,8 @@ SEQAN_CHECKPOINT
clear(intervals[i]);
++i;
}
- finish1 = clock();
- duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
+ // finish1 = clock();
+ //duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
//std::cout << "\ntook " << duration << " seconds.\n";
}
@@ -411,9 +411,9 @@
_makeAlignmentGraphFromRefinedSegments(String<std::set<TValue> > & all_nodes,
SEQAN_CHECKPOINT
//std::cout << "making refined alignment graph...";
//std::cout.flush();
- clock_t start, finish1;
- double duration;
- start = clock();
+ // clock_t start, finish1;
+ // double duration;
+ // start = clock();
//make nodes (same function for inexact and exact refinement)
_makeRefinedGraphNodes(all_nodes,seqs,ali_g);
@@ -425,8 +425,8 @@ SEQAN_CHECKPOINT
_makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag,revHack);
//std::cout << "check\n";
- finish1 = clock();
- duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
+ // finish1 = clock();
+ // duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
//std::cout << "\ntook " << duration << " seconds.\n";
}
--
2.3.5
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