[PATCH 03/10] comment out/remove unused vars
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 IteratorTAlignmentString,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 VertexDescriptorTGraph::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 =
[PATCH 06/10] provide dummy bodies for pure functions
From: Andrei Zavada johnhom...@gmail.com
in order for newer g++ to accept some template declarations
---
.../projects/library/seqan/file/file_format.h| 20
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/mugsy-seqan/projects/library/seqan/file/file_format.h
b/mugsy-seqan/projects/library/seqan/file/file_format.h
index 87212bf..d3d4271 100644
--- a/mugsy-seqan/projects/library/seqan/file/file_format.h
+++ b/mugsy-seqan/projects/library/seqan/file/file_format.h
@@ -136,27 +136,31 @@ public:
~FileFormat() {};
FileFormat const operator =(FileFormat const ) {}
+// flesh out the following methods in order to
+// let g++ accept this forward:
+// projects/library/seqan/file/file_generated_forwards.h:962:66:
error: invalid abstract return type 'seqan::FileFormatTFile, TData, TMeta,
void'
+// template typename TFile, typename TData, typename TMeta inline
FileFormatTFile, TData, TMeta, void guessFileFormat(TFile file, TData
data);// projects/library/seqan/file/file_form */
virtual void *
- formatID_() const = 0;
+ formatID_() const { return 0; }
virtual void
- read_(TFile file, TData data) const = 0;
+ read_(TFile file, TData data) const {}
virtual void
- read_(TFile file, TData data, TSize limit) const = 0;
+ read_(TFile file, TData data, TSize limit) const {}
virtual void
- readMeta_(TFile file, TMeta meta) const = 0;
+ readMeta_(TFile file, TMeta meta) const {}
virtual void
- goNext_(TFile file) const = 0;
+ goNext_(TFile file) const {}
virtual TSize
- length_(TFile file) const = 0;
+length_(TFile file) const { return (TSize)-1; }
virtual void
- write_(TFile file, TData data) const = 0;
+ write_(TFile file, TData data) const {}
virtual void
- write_(TFile file, TData data, TMeta meta) const = 0;
+ write_(TFile file, TData data, TMeta meta) const {}
};
--
2.3.5
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[PATCH 05/10] fix const-related warnings
From: Andrei Zavada johnhom...@gmail.com
---
MUMmer3.20/src/tigr/show-coords.cc| 2 +-
mugsy-seqan/projects/library/apps/mugsy/transformcoords.h | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/MUMmer3.20/src/tigr/show-coords.cc
b/MUMmer3.20/src/tigr/show-coords.cc
index 4a9bb7d..21d768b 100644
--- a/MUMmer3.20/src/tigr/show-coords.cc
+++ b/MUMmer3.20/src/tigr/show-coords.cc
@@ -788,7 +788,7 @@ void printBtab
(vectorAlignStats Stats)
{
time_t currtime;
- char * type;
+ const char * type;
char date[MAX_LINE];
long int len;
vectorAlignStats::iterator Sip;
diff --git a/mugsy-seqan/projects/library/apps/mugsy/transformcoords.h
b/mugsy-seqan/projects/library/apps/mugsy/transformcoords.h
index fc42939..3c060ee 100644
--- a/mugsy-seqan/projects/library/apps/mugsy/transformcoords.h
+++ b/mugsy-seqan/projects/library/apps/mugsy/transformcoords.h
@@ -31,6 +31,6 @@ extern C void parseSrcName(char* srcName, char* name, char*
src);
extern C struct mafFile *mafOpen(const char *fileName, int verbose);
extern C struct mafAli *mafNext(struct mafFile *mafFile);
extern C void mafWrite(FILE *f, struct mafAli *maf);
-extern C void mafWriteStart(FILE *f, char *scoring);
+extern C void mafWriteStart(FILE *f, const char *scoring);
extern C void mafFileFree(struct mafFile **pObj);
extern C void mafAliFree(struct mafAli **pObj);
--
2.3.5
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Re: Seqan knowledge needed (Was: Help needed in C++ / seqan issue)
Hi Andreas, Here's my take on mugsy issues. I worked on a tree checked out with: $ svn checkout svn://svn.code.sf.net/p/mugsy/code/trunk mugsy-code Building with gcc-4.9.2. The version of boost I compiled it against is 1.56. I couldn't get it to link, because the authors apparently never heard of autotools. Generally, those handwritten Makefile's just.. made me cry. Hope this helps, Andrei -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/1429929049-21676-1-git-send-email-andrei.zavada@gmail.com
[PATCH 02/10] comment out unused typedefs
From: Andrei Zavada johnhom...@gmail.com
---
mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp | 106 ++---
.../seqan/basic/basic_allocator_chunkpool.h| 2 +-
.../projects/library/seqan/basic/basic_holder.h| 10 +-
.../library/seqan/file/file_format_cgviz.h | 2 +-
.../projects/library/seqan/file/file_format_embl.h | 4 +-
.../library/seqan/file/file_format_fasta_align.h | 6 +-
.../projects/library/seqan/file/file_format_mmap.h | 6 +-
.../projects/library/seqan/file/file_format_sam.h | 4 +-
.../seqan/graph_algorithms/graph_algorithm.h | 18 ++--
.../seqan/graph_algorithms/graph_algorithm_hmm.h | 14 +--
.../graph_algorithms/graph_algorithm_lis_his.h | 2 +-
.../seqan/graph_align/graph_align_hirschberg.h | 4 +-
.../seqan/graph_msa/graph_align_tcoffee_base.h | 12 +--
.../seqan/graph_msa/graph_align_tcoffee_distance.h | 8 +-
.../graph_msa/graph_align_tcoffee_guidetree.h | 10 +-
.../seqan/graph_msa/graph_align_tcoffee_io.h | 36 +++
.../seqan/graph_msa/graph_align_tcoffee_library.h | 10 +-
.../seqan/graph_msa/graph_align_tcoffee_msa.h | 8 +-
.../graph_msa/graph_align_tcoffee_progressive.h| 16 ++--
.../graph_msa/graph_align_tcoffee_refinement.h | 10 +-
.../library/seqan/graph_types/graph_drawing.h | 10 +-
.../seqan/graph_types/graph_impl_automaton.h | 10 +-
.../library/seqan/graph_types/graph_impl_hmm.h | 14 +--
.../library/seqan/graph_types/graph_impl_oracle.h | 8 +-
.../library/seqan/graph_types/graph_impl_tree.h| 8 +-
.../library/seqan/graph_types/graph_impl_trie.h| 8 +-
.../seqan/graph_types/graph_impl_wordgraph.h | 4 +-
.../projects/library/seqan/map/map_skiplist.h | 6 +-
.../projects/library/seqan/map/sumlist_skip.h | 14 +--
.../seqan/modifier/modifier_alphabet_expansion.h | 4 +-
.../graph_algorithm_refine_exact_iterative.h | 10 +-
.../refinement/graph_algorithm_refine_inexact.h| 4 +-
.../library/seqan/refinement/graph_impl_align.h| 38
.../projects/library/seqan/sequence/lexical.h | 4 +-
.../library/seqan/sequence/sequence_multiple.h | 2 +-
.../projects/library/seqan/sequence/string_base.h | 24 ++---
.../library/seqan/sequence/string_packed.h | 2 +-
37 files changed, 229 insertions(+), 229 deletions(-)
diff --git a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
index 64fe0f7..7a3ba64 100644
--- a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
+++ b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
@@ -398,7 +398,7 @@ _cc_visit_g_ranked(GraphTSpec const g,
TSize maxdist)
{
//SEQAN_CHECKPOINT
- typedef typename IteratorGraphTSpec, AdjacencyIterator::Type
TAdjacencyIterator;
+ // typedef typename IteratorGraphTSpec, AdjacencyIterator::Type
TAdjacencyIterator;
typedef typename EdgeDescriptorGraphTSpec ::Type TEdgeDescriptor;
typedef typename IteratorGraphTSpec, OutEdgeIterator::Type
TOutEdgeIterator;
//Add all edges from u to ccedges
@@ -525,8 +525,8 @@
connected_components_by_genome_ranked_RECURSIVE(GraphTSpec const g,
typedef std::multimapTSize,TVertexDescriptor TGenomeVertexMap;
- typedef typename IteratorGraphTSpec, AdjacencyIterator::Type
TAdjacencyIterator;
- typedef typename IteratorGraphTSpec, OutEdgeIterator::Type
TOutEdgeIterator;
+ // typedef typename IteratorGraphTSpec, AdjacencyIterator::Type
TAdjacencyIterator;
+ // typedef typename IteratorGraphTSpec, OutEdgeIterator::Type
TOutEdgeIterator;
clear(components);
resizeVertexMap(g,components);
@@ -626,7 +626,7 @@ connected_components_by_genome_ranked(GraphTSpec const g,
typedef std::multimapTSize,TVertexDescriptor TGenomeVertexMap;
- typedef typename IteratorGraphTSpec, AdjacencyIterator::Type
TAdjacencyIterator;
+ // typedef typename IteratorGraphTSpec, AdjacencyIterator::Type
TAdjacencyIterator;
typedef typename IteratorGraphTSpec, OutEdgeIterator::Type
TOutEdgeIterator;
clear(components);
@@ -840,13 +840,13 @@ typename SizeGraphTSpec ::Type
connected_components_ranked(GraphTSpec const g,
TComponents components){
//SEQAN_CHECKPOINT
- typedef typename SizeGraphTSpec ::Type TSize;
+ // typedef typename SizeGraphTSpec ::Type TSize;
typedef typename IteratorGraphTSpec, EdgeIterator::Type TEdgeIterator;
typedef typename IteratorGraphTSpec, VertexIterator::Type
TVertexIterator;
typedef typename VertexDescriptorGraphTSpec ::Type TVertexDescriptor;
typedef typename EdgeDescriptorGraphTSpec ::Type TEdgeDescriptor;
- typedef typename IteratorGraphTSpec, AdjacencyIterator::Type
TAdjacencyIterator;
+ // typedef typename IteratorGraphTSpec, AdjacencyIterator::Type
TAdjacencyIterator;
typedef typename IteratorGraphTSpec,
[PATCH 07/10] enclose some logical expressions in parens for clarity
From: Andrei Zavada johnhom...@gmail.com
---
MUMmer3.20/src/tigr/repeat-match.cc | 2 +-
mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/MUMmer3.20/src/tigr/repeat-match.cc
b/MUMmer3.20/src/tigr/repeat-match.cc
index a4bf103..f7aa881 100644
--- a/MUMmer3.20/src/tigr/repeat-match.cc
+++ b/MUMmer3.20/src/tigr/repeat-match.cc
@@ -847,7 +847,7 @@ void List_Matches
{
if (Data [i - 1] == Data [j - 1]
|| Data [i + n] == Data [j + n]
- || i String_Separator j String_Separator)
+ || (i String_Separator j String_Separator))
continue;
Reversed = FALSE;
if (j String_Separator)
diff --git a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
index 177468e..da8f331 100644
--- a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
+++ b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
@@ -1187,7 +1187,7 @@ void doReadBlockFile(const std::string filename,
//Check if segment is reported as part of the LCB
//The LCB identification step may not report all sequences that
are part of the anchor
if(sequenceOrientMap.find(sname) != sequenceOrientMap.end()){
- if(!checkbounds ||
fragmentBegin(g,*vit)=sequenceCoordsMap[sname].first
fragmentBegin(g,*vit)=sequenceCoordsMap[sname].second){
+ if(!checkbounds ||
(fragmentBegin(g,*vit)=sequenceCoordsMap[sname].first
fragmentBegin(g,*vit)=sequenceCoordsMap[sname].second)){ // -Wuse-spacebar,
ffs!
vertexOrientMap[*vit] = sequenceOrientMap[sname];
//add node to block
currlcb.push_back(*vit);
--
2.3.5
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[PATCH 04/10] fix include names
From: Andrei Zavada johnhom...@gmail.com --- MUMmer3.20/src/tigr/show-diff.cc | 1 + chaining/synchain-mugsy.cpp | 7 +++ mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/MUMmer3.20/src/tigr/show-diff.cc b/MUMmer3.20/src/tigr/show-diff.cc index 421f20d..ea252d2 100644 --- a/MUMmer3.20/src/tigr/show-diff.cc +++ b/MUMmer3.20/src/tigr/show-diff.cc @@ -14,6 +14,7 @@ #include cstdlib #include cassert #include climits +#include algorithm using namespace std; diff --git a/chaining/synchain-mugsy.cpp b/chaining/synchain-mugsy.cpp index 669f017..1877ce4 100644 --- a/chaining/synchain-mugsy.cpp +++ b/chaining/synchain-mugsy.cpp @@ -80,8 +80,7 @@ #include list #include bitset #include algorithm -#include ext/hash_set //__gnu_cxx namespace -//#include tr1/unordered_set +#include set #include boost/graph/graphviz.hpp #include boost/graph/adjacency_list.hpp @@ -101,11 +100,11 @@ #include boost/graph/dijkstra_shortest_paths.hpp #include boost/graph/graph_traits.hpp #include boost/graph/properties.hpp -#include boost/property_map.hpp +#include boost/property_map/property_map.hpp #include boost/graph/breadth_first_search.hpp #include boost/graph/edmonds_karp_max_flow.hpp -#include boost/graph/kolmogorov_max_flow.hpp +#include boost/graph/boykov_kolmogorov_max_flow.hpp #include boost/graph/push_relabel_max_flow.hpp #include boost/graph/adjacency_list.hpp diff --git a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp index 7a3ba64..177468e 100644 --- a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp +++ b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp @@ -68,7 +68,7 @@ time_t lasttime; #include boost/graph/properties.hpp #include boost/graph/edmonds_karp_max_flow.hpp -#include boost/graph/kolmogorov_max_flow.hpp +#include boost/graph/boykov_kolmogorov_max_flow.hpp #include boost/graph/push_relabel_max_flow.hpp #include boost/graph/adjacency_list.hpp -- 2.3.5 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/1429929049-21676-5-git-send-email-andrei.zavada@gmail.com
[PATCH 08/10] drop names of unused args in function signatures
From: Andrei Zavada johnhom...@gmail.com
---
mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
index da8f331..a98f0cc 100644
--- a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
+++ b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
@@ -1704,8 +1704,8 @@ void convertCC2Blocks(TGraph g,
TComponentMap component,
std::mapstd::pairTComponent,TComponent,TBlock *
componentVertexMap,
std::vectorstd::vectorTBlock blocksbycomponent,
- std::mapTName,std::vectorTLoc aintervals,
- TNames sequenceNames){
+ std::mapTName,std::vectorTLoc ,
+ TNames ){
typedef typename IdTGraph::Type TIdType;
typedef typename VertexDescriptorTGraph::Type TVertexDescriptor;
--
2.3.5
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[PATCH 01/10] fix a -Wformat
From: Andrei Zavada johnhom...@gmail.com
---
MUMmer3.20/src/kurtz/libbasedir/space.c | 2 +-
MUMmer3.20/src/tigr/delta2blocks.cc | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/MUMmer3.20/src/kurtz/libbasedir/space.c
b/MUMmer3.20/src/kurtz/libbasedir/space.c
index 89dfec6..0f97fd4 100644
--- a/MUMmer3.20/src/kurtz/libbasedir/space.c
+++ b/MUMmer3.20/src/kurtz/libbasedir/space.c
@@ -379,7 +379,7 @@ void checkspaceleak(void)
}
if(numberofblocks 0)
{
-fprintf(stderr,space leak: number of blocks = %u\n,numberofblocks);
+fprintf(stderr,space leak: number of blocks = %lu\n, numberofblocks);
exit(EXIT_FAILURE);
}
free(blocks);
diff --git a/MUMmer3.20/src/tigr/delta2blocks.cc
b/MUMmer3.20/src/tigr/delta2blocks.cc
index a01bce8..13d8c83 100644
--- a/MUMmer3.20/src/tigr/delta2blocks.cc
+++ b/MUMmer3.20/src/tigr/delta2blocks.cc
@@ -405,7 +405,7 @@ void printAlignments
for ( Ap = Aligns.begin( ); Ap Aligns.end( ); Ap ++ )
{
- printf (%s %s %d %d %d %d ,IdR,IdQ, Ap-sR,Ap-eR,Ap-sQ,Ap-eQ);
+ printf (%s %s %ld %ld %ld %ld ,IdR,IdQ, Ap-sR,Ap-eR,Ap-sQ,Ap-eQ);
index++;
ct = 0;
sR = Ap-sR;
--
2.3.5
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[PATCH 09/10] wrap badly indented if-statements in {}, reindent
From: Andrei Zavada johnhom...@gmail.com
---
.../library/seqan/graph_msa/graph_align_tcoffee_io.h | 12 +++-
1 file changed, 7 insertions(+), 5 deletions(-)
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 0741c98..55f03be 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
@@ -514,11 +514,13 @@ templatetypename TValue, typename TSpec2, typename
TFragment, typename TSpec, t
else
++offset2;
} else ++offset1;
-} else if (value(mat, inseq2 * flen + col) != gapChar)
- if(orients[inseq2])
- ++offset2;//--offset2;
- else
- ++offset2;
+} else
+ if (value(mat, inseq2 * flen + col) != gapChar) {
+if(orients[inseq2])
+ ++offset2;//--offset2;
+else
+ ++offset2;
+ }
}
/*
//SVA append runs to matches
--
2.3.5
--
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[PATCH 10/10] cast to the type of rhs operand of a comparison operator
From: Andrei Zavada johnhom...@gmail.com
---
.../projects/library/seqan/refinement/graph_impl_interval_tree.h | 8
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git
a/mugsy-seqan/projects/library/seqan/refinement/graph_impl_interval_tree.h
b/mugsy-seqan/projects/library/seqan/refinement/graph_impl_interval_tree.h
index d924dd5..4474b8d 100644
--- a/mugsy-seqan/projects/library/seqan/refinement/graph_impl_interval_tree.h
+++ b/mugsy-seqan/projects/library/seqan/refinement/graph_impl_interval_tree.h
@@ -718,10 +718,10 @@ SEQAN_CHECKPOINT
{
TOutEdgeIterator it(g, act_knot);
act_prop = property(pm,act_knot);
- if(act_prop.center query)
+ if(act_prop.center (typeof act_prop.center)query)
{
unsigned int i = 0;
- while(i length(act_prop.list2)
rightBoundary(value(act_prop.list2,i)) query)
+ while(i length(act_prop.list2) (typeof
query)rightBoundary(value(act_prop.list2,i)) query)
{
appendValue(result,cargo(value(act_prop.list2,i)));
++i;
@@ -738,10 +738,10 @@ SEQAN_CHECKPOINT
act_knot = targetVertex(it);
}
else{
- if(query act_prop.center)
+ if(query (typeof query)act_prop.center)
{
unsigned int i = 0;
- while(i length(act_prop.list1)
leftBoundary(value(act_prop.list1,i)) = query)
+ while(i length(act_prop.list1) (typeof
query)leftBoundary(value(act_prop.list1,i)) = query)
{
appendValue(result,cargo(value(act_prop.list1,i)));
++i;
--
2.3.5
--
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