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Description: fix common gcc10 FTBFS issue
After fixing #957519 with no_std_hash_redefinition.patch, a few more issues
common to Gcc 10 cropped up. This patch addresses them.
Author: Étienne Mollier <etienne.mollier@mailoo.org>
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957519
Forwarded: no
Last-Update: 2020-10-13
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- mapsembler2.orig/kissreads/include/commons.h
+++ mapsembler2/kissreads/include/commons.h
@@ -49,26 +49,26 @@
#include<zlib.h>
typedef uint64_t kmer_type;
//int artificial_overlap;
-char comp ['t'+1];
-char nuc [4];
-char standard_fasta;
-char silent;
-char quality;
-int kmer_size;
-int size_seeds;
-int minimal_read_overlap;
-kmer_type mask_code_seed;
+__attribute__((__common__)) char comp ['t'+1];
+__attribute__((__common__)) char nuc [4];
+__attribute__((__common__)) char standard_fasta;
+__attribute__((__common__)) char silent;
+__attribute__((__common__)) char quality;
+__attribute__((__common__)) int kmer_size;
+__attribute__((__common__)) int size_seeds;
+__attribute__((__common__)) int minimal_read_overlap;
+__attribute__((__common__)) kmer_type mask_code_seed;
#ifdef INPUT_FROM_KISSPLICE
int min_overlap;
int countingOption;
#endif
int valid_character(const char c);
-int average_size_reads;
-int nb_event_sets;
-int number_of_read_sets;
-int size_before_reads_starting; // see fragment_info.h
-char * anykmer;
+extern int average_size_reads;
+extern int nb_event_sets;
+__attribute__((__common__)) int number_of_read_sets;
+extern int size_before_reads_starting; // see fragment_info.h
+__attribute__((__common__)) char * anykmer;
char ** sort_strings (char ** strings, int number);
void * mymalloc(const int size);
void * mycalloc(const int size, const int size_2);
@@ -86,14 +86,14 @@
int get_next_sequence_and_comments_for_fastq (gzFile file, char * sequence, char * comment, char * quality, char * line);
int get_next_sequence_for_fastq (gzFile file, char * read, char * quality, char * line);
int number_of_sequences_in_file(gzFile file, char * line);
-gzFile file;
+__attribute__((__common__)) gzFile file;
-uint64_t sum_memory;
-uint64_t sum_memory_strdup;
+__attribute__((__common__)) uint64_t sum_memory;
+__attribute__((__common__)) uint64_t sum_memory_strdup;
-uint64_t mask_nbseed ;
-uint64_t mask_offset_seed;
-unsigned int nbits_nbseeds;
+__attribute__((__common__)) uint64_t mask_nbseed ;
+__attribute__((__common__)) uint64_t mask_offset_seed;
+__attribute__((__common__)) unsigned int nbits_nbseeds;
// macro to test if a variable is null (i.e., a malloc failed)
#define test_alloc( variable) { if(variable == NULL){ fprintf(stderr,"cannot allocate memory for variable %s, exit\n",#variable); exit(1); }}
--- mapsembler2.orig/kissreads/include/fragment_index.h
+++ mapsembler2/kissreads/include/fragment_index.h
@@ -49,10 +49,10 @@
#include <couple.h>
-int number_of_starters;
-hash_t seeds; // hash table seed -> (fragment id, position)
-hash_t seeds_count;
-couple * seed_table;
+__attribute__((__common__)) int number_of_starters;
+__attribute__((__common__)) hash_t seeds; // hash table seed -> (fragment id, position)
+__attribute__((__common__)) hash_t seeds_count;
+__attribute__((__common__)) couple * seed_table;
p_fragment_info * index_starters_from_input_file (const int k, int nb_events_per_set, const int nb_fragment_per_event, const char input_only_upper, const int index_stride); // read and store all starters presents in the pointed file. Index by seeds of length k all these starters.
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