debian/changelog

+gatb-core (1.4.1+git20180206.6f8fce8+dfsg-1) unstable; urgency=medium
+
+  * New upstream commit to fit needs of minia and discosnp
+  * Add symbols file
+  * Bump SOVERSION due to changed symbols
+
+ -- Andreas Tille <tille@debian.org>  Tue, 22 Jan 2019 16:58:53 +0100
+
+gatb-core (1.4.1+dfsg-4) unstable; urgency=medium
+
+  * Install json.hpp since it is referenced in header files
+  * debhelper 12
+  * Standards-Version: 4.3.0
+
+ -- Andreas Tille <tille@debian.org>  Tue, 22 Jan 2019 14:50:38 +0100
+
 gatb-core (1.4.1+dfsg-3) unstable; urgency=medium
 
   * Make sure target dir exists also for Architecture: all build

debian/compat

-11
+12

debian/control

@@ -4,7 +4,7 @@ Uploaders: Nadiya Sitdykova <rovenskasa@gmail.com>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                d-shlibs,
                cmake,
                libcppunit-dev,
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
                libjsoncpp-dev,
                doxygen,
                graphviz
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/gatb-core
 Vcs-Git: https://salsa.debian.org/med-team/gatb-core.git
 Homepage: https://github.com/GATB/gatb-core
@@ -35,7 +35,7 @@ Description: Genome Analysis Toolbox with de-Bruijn graph
  exist a set of ready-to-use tools relying on GATB-CORE
  library: see https://gatb.inria.fr/software/
 
-Package: libgatbcore0
+Package: libgatbcore1
 Architecture: any
 Section: libs
 Depends: ${shlibs:Depends},
@@ -60,7 +60,7 @@ Architecture: any
 Section: libdevel
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         libgatbcore0 (= ${binary:Version})
+         libgatbcore1 (= ${binary:Version})
 Description: development library of the Genome Analysis Toolbox
  The GATB-CORE project provides a set of highly efficient
  algorithms to analyse NGS data sets. These methods enable

debian/libgatbcore-dev.install

+gatb-core/thirdparty/json	usr/include

debian/patches/0c580ab.patch

+From 0c580ab9e5f4a848c9c245060415e9acfe1655c7 Mon Sep 17 00:00:00 2001
+From: rchikhi <rayan.chikhi@univ-lille1.fr>
+Date: Mon, 24 Dec 2018 14:57:48 +0100
+Origin: https://github.com/GATB/gatb-core/commit/0c580ab.patch
+Subject: [PATCH] fixed bug #37 where unitigs are not output with consecutive
+ IDs, and also made sure that even if they're not, links are robust to that
+
+---
+ gatb-core/src/gatb/bcalm2/bglue_algo.cpp      | 19 ++++----------
+ gatb-core/src/gatb/bcalm2/bglue_algo.hpp      | 15 +++++++++--
+ gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp | 25 +++++++++++--------
+ 3 files changed, 32 insertions(+), 27 deletions(-)
+
+diff --git a/gatb-core/src/gatb/bcalm2/bglue_algo.cpp b/gatb-core/src/gatb/bcalm2/bglue_algo.cpp
+index 6256282e..c12d1f79 100644
+--- a/gatb-core/src/gatb/bcalm2/bglue_algo.cpp
++++ b/gatb-core/src/gatb/bcalm2/bglue_algo.cpp
+@@ -904,9 +904,7 @@ void bglue(Storage *storage,
+   
+     // setup output file
+     string output_prefix = prefix;
+-    std::atomic<unsigned long> out_id; // identified for output sequences
+-    out_id = 0;
+-    BufferedFasta out (output_prefix, 100000);
++    BufferedFasta out (output_prefix, 100000, true);
+ 
+     auto get_UFclass = [&modelCanon, &ufkmers_vector, &hasher, &uf_mphf]
+         (const string &kmerBegin, const string &kmerEnd,
+@@ -966,7 +964,7 @@ void bglue(Storage *storage,
+     std::mutex mtx; // lock to avoid a nasty bug when calling output()
+     auto partitionGlue = [k, &modelCanon /* crashes if copied!*/, \
+         &get_UFclass, &gluePartitions,
+-        &out, &outLock, &nb_seqs_in_partition, &out_id, nbGluePartitions, &mtx]
++        &out, &outLock, &nb_seqs_in_partition, nbGluePartitions, &mtx]
+             (const Sequence& sequence)
+     {
+         const string &seq = sequence.toString();
+@@ -992,12 +990,8 @@ void bglue(Storage *storage,
+             float mean_abundance = get_mean_abundance(abundances);
+             uint32_t sum_abundances = get_sum_abundance(abundances);
+             
+-            // for some reason i do need that lock_guard here.. even though output is itself lock guarded. maybe some lazyness in the evauation of the to_string(out_id++)? who kon
+-            // anyway this fixes the problem, i'll understand it some other time.
+-            std::lock_guard<std::mutex> lock(mtx);
+-            output(seq, out, std::to_string(out_id++) + " LN:i:" + to_string(seq.size()) + " KC:i:" + to_string(sum_abundances) + " km:f:" + to_string_with_precision(mean_abundance)); 
+             // km is not a standard GFA field so i'm putting it in lower case as per the spec
+-            // maybe could optimize by writing to disk using queues, if that's ever a bottleneck
++            output(seq, out, "LN:i:" + to_string(seq.size()) + " KC:i:" + to_string(sum_abundances) + " km:f:" + to_string_with_precision(mean_abundance)); 
+             return;
+         }
+ 
+@@ -1051,7 +1045,7 @@ void bglue(Storage *storage,
+     for (int partition = 0; partition < nbGluePartitions; partition++)
+     {
+         auto glue_partition = [&modelCanon, &ufkmers, partition, &gluePartition_prefix, nbGluePartitions, &copy_nb_seqs_in_partition,
+-        &get_UFclass, &out, &outLock, &out_id, kmerSize, &mtx]( int thread_id)
++        &get_UFclass, &out, &outLock, kmerSize, &mtx]( int thread_id)
+         {
+             int k = kmerSize;
+ 
+@@ -1140,10 +1134,7 @@ void bglue(Storage *storage,
+                 float mean_abundance = get_mean_abundance(abs);
+                 uint32_t sum_abundances = get_sum_abundance(abs);
+                 {
+-                    // for some reason i do need that lock_guard here.. even though output is itself lock guarded. maybe some lazyness in the evauation of the to_string(out_id++)? who kon
+-                    // anyway this fixes the problem, i'll understand it some other time.
+-                    std::lock_guard<std::mutex> lock(mtx);
+-                    output(seq, out, std::to_string(out_id++) + " LN:i:" + to_string(seq.size()) + " KC:i:" + to_string(sum_abundances) + " km:f:" + to_string_with_precision(mean_abundance)); 
++                    output(seq, out, "LN:i:" + to_string(seq.size()) + " KC:i:" + to_string(sum_abundances) + " km:f:" + to_string_with_precision(mean_abundance));
+                 }
+             }
+                 
+diff --git a/gatb-core/src/gatb/bcalm2/bglue_algo.hpp b/gatb-core/src/gatb/bcalm2/bglue_algo.hpp
+index 50ca9176..7783215f 100644
+--- a/gatb-core/src/gatb/bcalm2/bglue_algo.hpp
++++ b/gatb-core/src/gatb/bcalm2/bglue_algo.hpp
+@@ -43,16 +43,21 @@ class BufferedFasta
+         std::string buffer;
+         unsigned long buffer_length;
+         FILE* _insertHandle;
++        bool needs_consecutive_ids;
++        unsigned long consecutive_id;
+ 
+     public:
+         unsigned long max_buffer;
+         bool threadsafe;
+ 
+-        BufferedFasta(const std::string filename, unsigned long given_max_buffer = 50000)
++        BufferedFasta(const std::string filename, unsigned long given_max_buffer = 50000, bool given_needs_consecutive_ids = false)
+         {
+             max_buffer = given_max_buffer; // that much of buffering will be written to the file at once (in bytes)
+             threadsafe = true;
+             buffer_length = 0;
++            consecutive_id = 0;
++            needs_consecutive_ids = given_needs_consecutive_ids;
++            if ((!threadsafe) && needs_consecutive_ids) { std::cout << "error, non-threadsafe bufferedfasta with consecutive ids asked" << std::endl; exit(1);}
+             _insertHandle = fopen (filename.c_str(), "w");
+             if (!_insertHandle) { std::cout << "error opening " << filename << " for writing." << std::endl; exit(1);}
+             buffer.reserve(max_buffer+1000/*security*/);
+@@ -73,7 +78,13 @@ class BufferedFasta
+             if (buffer_length + insert_size > max_buffer)
+                 flush();
+             buffer_length += insert_size;
+-            buffer += ">" + comment + "\n" + seq + "\n";
++            buffer += ">";
++            if (needs_consecutive_ids)
++            {
++                buffer += std::to_string(consecutive_id) + " "; 
++                consecutive_id++;
++            }
++            buffer += comment + "\n" + seq + "\n";
+             if (threadsafe)
+                 mtx.unlock();
+         }
+diff --git a/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp b/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp
+index a13668ac..b21d164e 100644
+--- a/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp
++++ b/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp
+@@ -41,6 +41,9 @@ namespace gatb { namespace core { namespace debruijn { namespace impl  {
+  * it uses the disk to store the links for extremities until they're merged into the final unitigs file. 
+  *
+  * so the memory usage is just that of the hash tables that record kmers, not of the links
++ *
++ * Assumption: FASTA header of unitigs starts with a unique number (unitig ID). 
++ * Normally bcalm outputs consecutive unitig ID's but LinkTigs could also work with non-consecutive, non-sorted IDs
+  */
+ template<size_t span>
+ void link_tigs(string unitigs_filename, int kmerSize, int nb_threads, uint64_t &nb_unitigs, bool verbose)
+@@ -219,7 +222,6 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa
+ 
+     BankFasta inputBank (unitigs_filename);
+     BankFasta::Iterator itSeq (inputBank);
+-    uint64_t utig_counter = 0;
+     
+     Model modelKminusOne(kmerSize - 1); // it's canonical (defined in the .hpp file)
+     
+@@ -235,12 +237,15 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa
+         const string& seq = itSeq->toString();
+         if (debug) std::cout << "unitig: " << seq << std::endl;
+ 
++        const string& comment = itSeq->getComment();        
++        unsigned long utig_id = std::stoul(comment.substr(0, comment.find(' ')));
++        
+         if (is_in_pass(seq, pass, UNITIG_BEGIN, kmerSize))
+         { 
+             if (debug) std::cout << "pass " << pass << " examining beginning" << std::endl;
+             typename Model::Kmer kmerBegin = modelKminusOne.codeSeed(seq.substr(0, kmerSize-1).c_str(), Data::ASCII);
+             bool beginInSameOrientation = modelKminusOne.toString(kmerBegin.value()) == seq.substr(0,kmerSize-1);
+-            ExtremityInfo eBegin(utig_counter, !beginInSameOrientation /* because we record rc*/, UNITIG_BEGIN);
++            ExtremityInfo eBegin(utig_id, !beginInSameOrientation /* because we record rc*/, UNITIG_BEGIN);
+             utigs_links_map[kmerBegin.value()].push_back(eBegin.pack());
+         }
+         if (is_in_pass(seq, pass, UNITIG_END, kmerSize))
+@@ -248,11 +253,10 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa
+             if (debug) std::cout << "pass " << pass << " examining end" << std::endl;
+             typename Model::Kmer kmerEnd = modelKminusOne.codeSeed(seq.substr(seq.size() - kmerSize+1).c_str(), Data::ASCII);
+             bool endInSameOrientation = modelKminusOne.toString(kmerEnd.value()) == seq.substr(seq.size() - kmerSize+1);
+-            ExtremityInfo eEnd(  utig_counter, !endInSameOrientation,                             UNITIG_END);
++            ExtremityInfo eEnd(  utig_id, !endInSameOrientation,                             UNITIG_END);
+             utigs_links_map[kmerEnd.value()].push_back(eEnd.pack());
+             // there is no UNITIG_BOTH here because we're taking (k-1)-mers.
+         }
+-        utig_counter++;
+     }
+ 
+     std::ofstream links_file(unitigs_filename+".links." +to_string(pass));
+@@ -262,12 +266,13 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa
+         nb_hashed_entries += v.second.size(); 
+     logging("step 2 (" + to_string(utigs_links_map.size()) + "kmers/" + to_string(nb_hashed_entries) + "extremities)");
+ 
+-    utig_counter = 0;
+     for (itSeq.first(); !itSeq.isDone(); itSeq.next()) 
+     {
+         const string& seq = itSeq->toString();
+-        
+-        if (debug) std::cout << "unitig: " << seq << std::endl;
++        const string& comment = itSeq->getComment();        
++        unsigned long utig_id = std::stoul(comment.substr(0, comment.find(' ')));
++
++        if (debug) std::cout << "unitig "  << std::to_string(utig_id)  << " : " << seq << std::endl;
+  
+         if (is_in_pass(seq, pass, UNITIG_BEGIN, kmerSize))
+         {
+@@ -324,7 +329,7 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa
+                 if (debug) std::cout << std::endl;
+             }
+             
+-            record_links(utig_counter, pass, in_links, links_file);
++            record_links(utig_id, pass, in_links, links_file);
+         }
+ 
+ 
+@@ -371,10 +376,8 @@ void link_unitigs_pass(const string unitigs_filename, bool verbose, const int pa
+                 }
+                 if (debug) std::cout << std::endl;
+             }
+-            record_links(utig_counter, pass, out_links, links_file);
++            record_links(utig_id, pass, out_links, links_file);
+         }
+-
+-        utig_counter++;
+     }
+ }
+ 

debian/patches/44d5a44.patch

+From 44d5a444f7d8b921b66065ef2d6270d3eb0f1446 Mon Sep 17 00:00:00 2001
+From: rchikhi <rayan.chikhi@univ-lille1.fr>
+Date: Tue, 25 Dec 2018 01:05:20 +0100
+Origin: https://github.com/GATB/gatb-core/commit/44d5a44.patch
+Subject: [PATCH] fixed kmer counting of IUPAC nucleotides
+
+---
+ gatb-core/src/gatb/tools/misc/api/Data.cpp |  4 ++++
+ gatb-core/src/gatb/tools/misc/api/Data.hpp | 21 +++++++++++++++++----
+ 2 files changed, 21 insertions(+), 4 deletions(-)
+ create mode 100644 gatb-core/src/gatb/tools/misc/api/Data.cpp
+
+diff --git a/gatb-core/src/gatb/tools/misc/api/Data.cpp b/gatb-core/src/gatb/tools/misc/api/Data.cpp
+new file mode 100644
+index 00000000..cddc7e38
+--- /dev/null
++++ b/gatb-core/src/gatb/tools/misc/api/Data.cpp
+@@ -0,0 +1,4 @@
++#include <gatb/tools/misc/api/Data.hpp>
++
++const unsigned char gatb::core::tools::misc::Data::validNucleotide[]= {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1};
++
+diff --git a/gatb-core/src/gatb/tools/misc/api/Data.hpp b/gatb-core/src/gatb/tools/misc/api/Data.hpp
+index 0c39e726..22e174a3 100644
+--- a/gatb-core/src/gatb/tools/misc/api/Data.hpp
++++ b/gatb-core/src/gatb/tools/misc/api/Data.hpp
+@@ -170,17 +170,30 @@ class Data : public Vector<char>
+      *  - second : 0 if valid, 1 if invalid (in case of N character for instance) */
+     typedef std::pair<char,char> ConvertChar;
+ 
+-    /** Note for the ASCII conversion: the 4th bit is used to tell whether it is invalid or not.
+-     * => it finds out that 'N' character has this 4th bit equals to 1, which is not the case
+-     * for 'A', 'C', 'G' and 'T'. */
+-    struct ConvertASCII    { static ConvertChar get (const char* buffer, size_t idx)  { return ConvertChar((buffer[idx]>>1) & 3, (buffer[idx]>>3) & 1); }};
++    /** Used to have the following trick:
++     *   (buffer[idx]>>3)& 1
++     * was equal to 1 for 'A', 'C', 'G' and 'T' (and also the lower case version)
++     * and was equal to 0 for 'N' and 'n' 
++     * but unfortunately it doesn't work for some of the IUPAC codes, like 'R' 
++     * */
++    struct ConvertASCII    { static ConvertChar get (const char* buffer, size_t idx)  { return ConvertChar((buffer[idx]>>1) & 3, validNucleotide[(unsigned char)(buffer[idx])]); }};
+     struct ConvertInteger  { static ConvertChar get (const char* buffer, size_t idx)  { return ConvertChar(buffer[idx],0); }         };
+     struct ConvertBinary   { static ConvertChar get (const char* buffer, size_t idx)  { return ConvertChar(((buffer[idx>>2] >> ((3-(idx&3))*2)) & 3),0); } };
+ 
++    static const unsigned char validNucleotide[];
+ private:
+ 
+     /** Encoding scheme of the data instance. */
+     Encoding_e  encoding;
++
++    /* generated using:
++     * codes=[1]*256
++     * codes[ord('A')] = codes[ord('a')] = 0;
++     * codes[ord('C')] = codes[ord('c')] = 0;
++     * codes[ord('G')] = codes[ord('g')] = 0;
++     * codes[ord('T')] = codes[ord('t')] = 0;
++     * print(codes)
++     */
+ };
+ 
+ /********************************************************************************/

debian/patches/5d45664.patch

+From 5d4566430e0f708b602d26e0b54bd21dd4d7852b Mon Sep 17 00:00:00 2001
+From: rchikhi <rayan.chikhi@univ-lille1.fr>
+Date: Sat, 20 Oct 2018 10:30:53 +0200
+Origin: https://github.com/GATB/gatb-core/commit/5d45664.patch
+Subject: [PATCH] fix typo gatb/minia#11
+
+---
+ gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp b/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp
+index 96cf3b2f..a86969f5 100644
+--- a/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp
++++ b/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp
+@@ -212,7 +212,7 @@ IOptionsParser* SortingCountAlgorithm<span>::getOptionsParser (bool mandatory)
+     parser->push_back (new OptionOneParam (STR_KMER_ABUNDANCE_MIN_THRESHOLD,"min abundance hard threshold (only used when min abundance is \"auto\")",false, "2"));
+     parser->push_back (new OptionOneParam (STR_HISTOGRAM_MAX,     "max number of values in kmers histogram",        false, "10000"));
+     parser->push_back (new OptionOneParam (STR_SOLIDITY_KIND,     "way to compute counts of several files (sum, min, max, one, all, custom)",false, "sum"));
+-	parser->push_back (new OptionOneParam (STR_SOLIDITY_CUSTOM,   "when solidity-kind is cutom, specifies list of files where kmer must be present",false, ""));
++	parser->push_back (new OptionOneParam (STR_SOLIDITY_CUSTOM,   "when solidity-kind is custom, specifies list of files where kmer must be present",false, ""));
+     parser->push_back (new OptionOneParam (STR_MAX_MEMORY,        "max memory (in MBytes)",                         false, "5000"));
+     parser->push_back (new OptionOneParam (STR_MAX_DISK,          "max disk   (in MBytes)",                         false, "0"));
+     parser->push_back (new OptionOneParam (STR_URI_SOLID_KMERS,   "output file for solid kmers (only when constructing a graph)", false));

debian/patches/61c5ee1.patch

+From 61c5ee19d44812f506258c22177c684936f8fd6f Mon Sep 17 00:00:00 2001
+From: rchikhi <rayan.chikhi@univ-lille1.fr>
+Date: Mon, 22 Oct 2018 11:48:08 +0200
+Origin: https://github.com/GATB/gatb-core/commit/61c5ee1.patch
+Subject: [PATCH] small bugfix
+
+---
+ gatb-core/test/unit/src/debruijn/TestDebruijn.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp b/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp
+index 1be96659..8d12e1fa 100644
+--- a/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp
++++ b/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp
+@@ -1298,7 +1298,7 @@ class TestDebruijn : public Test
+ 
+         Node n2 = graph.reverse (n1);
+         CPPUNIT_ASSERT (n2.strand == STRAND_REVCOMP);
+-        CPPUNIT_ASSERT (graph.toString(n2).compare ("TCAG") == 0 ||  graph.toString(n1).compare ("TGGA") == 0);
++        CPPUNIT_ASSERT (graph.toString(n2).compare ("TCAG") == 0 ||  graph.toString(n2).compare ("TGGA") == 0);
+     }
+ 
+ 

debian/patches/da4ceed.patch

+From da4ceed164c761ad264b5b0b4e6745a9d9e33ea0 Mon Sep 17 00:00:00 2001
+From: rchikhi <rayan.chikhi@univ-lille1.fr>
+Date: Mon, 24 Dec 2018 15:12:41 +0100
+Origin: https://github.com/GATB/gatb-core/commit/da4ceed.patch
+Subject: [PATCH] minor cleanup
+
+---
+ gatb-core/src/gatb/bcalm2/bglue_algo.cpp | 5 ++---
+ 1 file changed, 2 insertions(+), 3 deletions(-)
+
+diff --git a/gatb-core/src/gatb/bcalm2/bglue_algo.cpp b/gatb-core/src/gatb/bcalm2/bglue_algo.cpp
+index c12d1f79..6c1ec575 100644
+--- a/gatb-core/src/gatb/bcalm2/bglue_algo.cpp
++++ b/gatb-core/src/gatb/bcalm2/bglue_algo.cpp
+@@ -961,10 +961,9 @@ void bglue(Storage *storage,
+ 
+ 
+     // partition the glue into many files, à la dsk
+-    std::mutex mtx; // lock to avoid a nasty bug when calling output()
+     auto partitionGlue = [k, &modelCanon /* crashes if copied!*/, \
+         &get_UFclass, &gluePartitions,
+-        &out, &outLock, &nb_seqs_in_partition, nbGluePartitions, &mtx]
++        &out, &outLock, &nb_seqs_in_partition, nbGluePartitions]
+             (const Sequence& sequence)
+     {
+         const string &seq = sequence.toString();
+@@ -1045,7 +1044,7 @@ void bglue(Storage *storage,
+     for (int partition = 0; partition < nbGluePartitions; partition++)
+     {
+         auto glue_partition = [&modelCanon, &ufkmers, partition, &gluePartition_prefix, nbGluePartitions, &copy_nb_seqs_in_partition,
+-        &get_UFclass, &out, &outLock, kmerSize, &mtx]( int thread_id)
++        &get_UFclass, &out, &outLock, kmerSize]( int thread_id)
+         {
+             int k = kmerSize;
+ 

debian/patches/fix_install_location.patch

@@ -4,15 +4,16 @@ Description: Install examples into correct dir
 
 --- a/gatb-core/CMakeLists.txt
 +++ b/gatb-core/CMakeLists.txt
-@@ -284,16 +284,17 @@ IF (EXISTS "${PROJECT_SOURCE_DIR}/exampl
-     ENDIF()
- ENDIF()
+@@ -286,7 +286,7 @@ ENDIF()
+ 
+ IF (NOT DEFINED GATB_CORE_EXCLUDE_EXAMPLES)
      # add example snippets into binary archive (use by CPack directive)
 -    INSTALL(DIRECTORY "${PROJECT_SOURCE_DIR}/examples/" DESTINATION "examples")
 +    INSTALL(DIRECTORY "${PROJECT_SOURCE_DIR}/examples/" DESTINATION "share/doc/gatb-core/examples")
+ ENDIF()
  
  ################################################################################
- #  INSTALL 
+@@ -294,9 +294,10 @@ ENDIF()
  ################################################################################
  
  IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)

debian/patches/series

@@ -6,3 +6,8 @@ set_soversion.patch
 dynamic_linking_of_tools.patch
 multiarch.patch
 spelling.patch
+#44d5a44.patch
+#da4ceed.patch
+#0c580ab.patch
+#61c5ee1.patch
+#5d45664.patch

debian/patches/set_soversion.patch

@@ -9,7 +9,7 @@ Description: Invent soversion 0 since upstream does not set soversion
  
  set_target_properties  (gatbcore-static   PROPERTIES OUTPUT_NAME  gatbcore  clean_direct_output 1)
 -set_target_properties (gatbcore-dynamic  PROPERTIES OUTPUT_NAME  gatbcore  clean_direct_output 1)
-+set_target_properties (gatbcore-dynamic  PROPERTIES OUTPUT_NAME  gatbcore  SOVERSION 0   clean_direct_output 1)
++set_target_properties (gatbcore-dynamic  PROPERTIES OUTPUT_NAME  gatbcore  SOVERSION 1   clean_direct_output 1)
  
  ################################################################################
  #  INSTALLATION 

debian/patches/spelling.patch

@@ -4,7 +4,7 @@ Description: Fix spelling issues
 
 --- a/gatb-core/src/gatb/tools/compression/DnaCoder.cpp
 +++ b/gatb-core/src/gatb/tools/compression/DnaCoder.cpp
-@@ -647,7 +647,7 @@ void DnaEncoder::encodeAnchorRead(int an
+@@ -650,7 +650,7 @@ void DnaEncoder::encodeAnchorRead(int an
  		//CompressionUtils::encodeNumeric(_rangeEncoder, _isPrevReadAnchorablePosModel, _isPrevReadAnchorablePos);
  		//}
  	//_prevAnchorAddress = anchorAddress;
@@ -13,7 +13,7 @@ Description: Fix spelling issues
  
  	
  	kmer_type anchor = _kmers[anchorPos];
-@@ -1491,7 +1491,7 @@ void DnaDecoder::decodeAnchorRead(){
+@@ -1494,7 +1494,7 @@ void DnaDecoder::decodeAnchorRead(){
  	#ifdef PRINT_DEBUG_DECODER
  		cout << "\t\t\tRead size: " << _readSize << endl;
  		cout << "\t\t\tAnchor pos: " << anchorPos << endl;

debian/patches/use_debian_packaged_hdf5.patch

@@ -13,7 +13,7 @@ Description: Use Debian packaged hdf5
  ##########  MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED  ##########
  SET (HDF5_BUILD_TOOLS             ON CACHE BOOL "Build HDF5 Tools")
  #SET (CMAKE_EXE_LINKER_FLAGS       "-lpthread -lz")
-@@ -16,9 +18,9 @@
+@@ -16,9 +18,9 @@ SET (HDF5_EXTERNALLY_CONFIGURED     ON)
  SET (HDF5_INSTALL_BIN_DIR           bin)
  SET (HDF5_INSTALL_LIB_DIR           lib)
  
@@ -26,7 +26,7 @@ Description: Use Debian packaged hdf5
  
  IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
      SET (HDF5_EXPORTED_TARGETS          "gatb-hdf5")
-@@ -32,23 +34,6 @@
+@@ -32,23 +34,6 @@ ENDIF()
  set (COMPILE_DEFINITIONS  "${COMPILE_DEFINITIONS}  -w")
  add_definitions (${COMPILE_DEFINITIONS})
  
@@ -50,7 +50,7 @@ Description: Use Debian packaged hdf5
  # include other smaller libraries (json, Boophf)
  
  add_custom_target (thirdparty_copy ALL)
-@@ -63,7 +48,5 @@
+@@ -63,7 +48,5 @@ add_custom_command (TARGET thirdparty_co
  #  INSTALL 
  ################################################################################
  IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
@@ -60,7 +60,7 @@ Description: Use Debian packaged hdf5
  ENDIF ()
 --- a/gatb-core/CMakeLists.txt
 +++ b/gatb-core/CMakeLists.txt
-@@ -99,7 +99,7 @@
+@@ -99,7 +99,7 @@ endif()
  # GENERAL DEFINITIONS
  ################################################################################
  set (LIBRARY_COMPILE_DEFINITIONS "-std=c++11")
@@ -69,7 +69,7 @@ Description: Use Debian packaged hdf5
  
  if (CMAKE_BUILD_TYPE STREQUAL "Debug")
      set (debug 1)
-@@ -211,16 +211,23 @@
+@@ -211,16 +211,23 @@ set (gatb-core-flags ${LIBRARY_COMPILE_D
  set (gatb-core-includes ${PROJECT_BINARY_DIR}/include  ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE} ${PROJECT_SOURCE_DIR}/src  ${PROJECT_SOURCE_DIR}/thirdparty ${gatb-core-extra-libraries-inc})
  
  # We define the libraries used for linking binary based on gatb core
@@ -99,7 +99,7 @@ Description: Use Debian packaged hdf5
  
  ################################################################################
  #  LIBRARY GENERATION 
-@@ -253,11 +260,13 @@
+@@ -253,11 +260,13 @@ ENDIF()
  ################################################################################
  ADD_SUBDIRECTORY(thirdparty)
  
@@ -118,7 +118,7 @@ Description: Use Debian packaged hdf5
  
  ################################################################################
  #  DOCUMENTATION GENERATION 
-@@ -285,7 +294,7 @@
+@@ -288,7 +297,7 @@ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUD
      INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt  DESTINATION . OPTIONAL)
      INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE              DESTINATION . OPTIONAL)
      INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md      DESTINATION . OPTIONAL)

debian/rules

@@ -16,7 +16,6 @@ override_dh_auto_build-indep:
 	echo "Save time of autobuilders and do nothing ... unfortunately this does not seem to work"
 
 override_dh_install-arch:
-	dh_install -a
 	d-shlibmove --commit \
 		    --multiarch \
 		    --devunversioned \
@@ -25,6 +24,7 @@ override_dh_install-arch:
                     --movedev gatb-core/cmake usr/lib \
                     debian/tmp/usr/lib/*/*.so
 	mkdir -p debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)
+	dh_install -a
 
 override_dh_install-indep:
 	dh_install -i

gatb-core/.gitignore

-CMakeLists.txt.user
-/build*
-/.settings/
-/.cproject
-*.leon
-.DS_Store
-

gatb-core/CMakeLists.txt

@@ -274,8 +274,11 @@ IF (EXISTS "${PROJECT_SOURCE_DIR}/examples")
         ADD_SUBDIRECTORY(examples)
     ENDIF()
 ENDIF()
+
+IF (NOT DEFINED GATB_CORE_EXCLUDE_EXAMPLES)
     # add example snippets into binary archive (use by CPack directive)
     INSTALL(DIRECTORY "${PROJECT_SOURCE_DIR}/examples/" DESTINATION "examples")
+ENDIF()
 
 ################################################################################
 #  INSTALL 

gatb-core/doc/book/.gitignore

-/main.aux
-/main.log
-/main.pdf

gatb-core/src/gatb/bank/api/IBank.hpp

@@ -92,6 +92,10 @@ public:
 	 * \return estimation of the number of sequences of sub bank i */
 	virtual int64_t estimateNbItemsBanki (int i) = 0;
 	
+	/** Return the vector of  sub IBank objects (in case of bank composite), or a vector containing only the bank itself
+	 * \return the IBank objects. */
+	virtual const std::vector<IBank*> getBanks() const  = 0;
+	
     /** \copydoc tools::collections::Iterable::iterator */
     virtual tools::dp::Iterator<Sequence>* iterator () = 0;