Commit 8e45a9a1 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.4.1+dfsg

parent 51eb9b0b

gatb-core/CMakeLists.txt

+1 −1
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@@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 3.1.0) 
# The default version number is the latest official build

SET (gatb-core_VERSION_MAJOR 1)

SET (gatb-core_VERSION_MINOR 4)

SET (gatb-core_VERSION_PATCH 0)

SET (gatb-core_VERSION_PATCH 1)



# But, it is possible to define another release number during a local build

IF (DEFINED MAJOR)

gatb-core/RELEASES.md

+8 −0
Original line number Diff line number Diff line 
--------------------------------------------------------------------------------

# RELEASE 1.4.1



* This is a bugfix release

	* fixed a segfault in some multi-threaded situations

	* removed some spurious large files in the distrib

	* fixed a bug with the -storate-type file option



--------------------------------------------------------------------------------

# RELEASE 1.4.0

gatb-core/src/gatb/bcalm2/bglue_algo.cpp

+16 −6
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@@ -791,7 +791,10 @@ void bglue(Storage *storage, 
        const typename ModelCanon::Kmer kmmerBegin = modelCanon.codeSeed(kmerBegin.c_str(), Data::ASCII);

        const typename ModelCanon::Kmer kmmerEnd = modelCanon.codeSeed(kmerEnd.c_str(), Data::ASCII);



        ufkmers.union_(uf_mphf.lookup(hasher(kmmerBegin)), uf_mphf.lookup(hasher(kmmerEnd)));

        uint32_t v1 = uf_mphf.lookup(hasher(kmmerBegin));

        uint32_t v2 = uf_mphf.lookup(hasher(kmmerEnd));



        ufkmers.union_(v1,v2);

        //ufkmers.union_((hasher(kmmerBegin)), (hasher(kmmerEnd)));



#if 0
@@ -818,7 +821,6 @@ void bglue(Storage *storage, 


    };



    //setDispatcher (new SerialDispatcher()); // force single thread

    Dispatcher dispatcher (nb_threads);

    dispatcher.iterate (in->iterator(), createUF);
@@ -836,6 +838,7 @@ void bglue(Storage *storage, 
    if (debug_uf_stats) // for debugging

    {

        ufkmers.printStats("uf kmers");

        //ufkmers.dumpUF("uf.dump");

        logging("after computing UF stats");

    }
@@ -929,6 +932,7 @@ void bglue(Storage *storage, 


    logging( "Allowed " + to_string((max_buffer * nbGluePartitions) /1024 /1024) + " MB memory for buffers");





    // partition the glue into many files, à la dsk

    auto partitionGlue = [k, &modelCanon /* crashes if copied!*/, \

        &get_UFclass, &gluePartitions,
@@ -1010,10 +1014,11 @@ void bglue(Storage *storage, 


    // glue all partitions using a thread pool

    ThreadPool pool(nb_threads);

    std::mutex mtx; // lock to avoid a nasty bug when calling output()

    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]( int thread_id)

        &get_UFclass, &out, &outLock, &out_id, kmerSize, &mtx]( int thread_id)

        {

            int k = kmerSize;
@@ -1101,8 +1106,13 @@ 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)); 

                }

            }

                

            free_memory_vector(ordered_sequences_idxs);

gatb-core/src/gatb/bcalm2/ograph.cpp

+1 −1
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@@ -126,7 +126,7 @@ template<size_t span> 
void graph3<span>::compaction(uint iL,  uint iR,typename graph3<span>::kmerType kmmer){

	if(iR!=iL){

		typename graph3<span>::kmerType RC=rcb(kmmer);

		uint s1(unitigs[iL].size()),s2(unitigs[iR].size());

		//uint s1(unitigs[iL].size()),s2(unitigs[iR].size());

		bool b1(isNumber(unitigs[iL][0])),b2(isNumber(unitigs[iR][0]));

		if(b1 and b2){return compaction(stoi(unitigs[iL]),stoi(unitigs[iR]),kmmer);}

		if(b1){return compaction(stoi(unitigs[iL]),iR,kmmer);}

gatb-core/src/gatb/bcalm2/unionFind.hpp

+10 −0
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@@ -5,6 +5,7 @@ 
#include <set>

#include <atomic>

#include <iostream>

#include <fstream>

#include <unordered_map>



/**
@@ -130,6 +131,15 @@ public: 
        std::cout << "raw space of UF hash data: " << ( 2*getNumKeys * sizeof(T)  ) /1024/1024 << " MB" << std::endl; // 2x because each key of type T is associated to a value of type T

    }



    // debug function

    void dumpUF(std::string file)

    {

        std::ofstream dumpfile;

        dumpfile.open (file);

        for (uint32_t i=0; i<size(); ++i)

            dumpfile << i << " " << mData[i]  << std::endl;

        dumpfile.close();

    }





    mutable std::vector<std::atomic<uint64_t>> mData;