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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/kissplice">Debian Med / kissplice</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/kissplice/-/commit/7fa562e547544b6bf14a38fe3fe05bc0be309197">7fa562e5</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-10-26T03:25:05+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Attempt to fix gcc-10 FTBFS
</pre>
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<h4>2 changed files:</h4>
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<a href="#81a9a5b123fb5e9473f68e4733e9d389fa7872c9">
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+
debian/patches/gcc10.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="81a9a5b123fb5e9473f68e4733e9d389fa7872c9">
<a href="https://salsa.debian.org/med-team/kissplice/-/commit/7fa562e547544b6bf14a38fe3fe05bc0be309197#81a9a5b123fb5e9473f68e4733e9d389fa7872c9"><strong>debian/patches/gcc10.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/thirdparty/kissreads/include/commons.h</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/thirdparty/kissreads/include/commons.h</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -49,28 +49,28 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> #include<zlib.h></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> typedef uint64_t kmer_type;</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> //int artificial_overlap;</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char comp ['t'+1];</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char nuc [4];</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char standard_fasta;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char silent;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char quality;</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char only_print;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int kmer_size;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int size_seeds;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int minimal_read_overlap;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-kmer_type mask_code_seed;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) char comp ['t'+1];</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) char nuc [4];</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) char standard_fasta;</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) char silent;</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) char quality;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) char only_print;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) int kmer_size;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) int size_seeds;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) int minimal_read_overlap;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) kmer_type mask_code_seed;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> #ifdef INPUT_FROM_KISSPLICE</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int kisspliceKmerSize;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int min_overlap;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int countingOption;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) int kisspliceKmerSize;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) int min_overlap;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) int countingOption;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> int valid_character(const char c);</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int average_size_reads;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int nb_event_sets;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int number_of_read_sets;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int size_before_reads_starting; // see fragment_info.h</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-char * anykmer;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern int average_size_reads;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern int nb_event_sets;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) int number_of_read_sets;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern int size_before_reads_starting; // see fragment_info.h</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) char * anykmer;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> char ** sort_strings (char ** strings, int number);</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> void * mymalloc(const int size);</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> void * mycalloc(const int size, const int size_2);</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="p">@@ -89,14 +89,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> int get_next_sequence_and_comments_for_fastq (gzFile file, char * sequence, char * comment, char * quality, char * line);</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> int get_next_sequence_for_fastq (gzFile file, char * read, char * quality, char * readid, char * qualityid);</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> int number_of_sequences_in_file(gzFile file, char * line);</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-gzFile file;</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) gzFile file;</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-uint64_t sum_memory;</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-uint64_t sum_memory_strdup;</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) uint64_t sum_memory;</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) uint64_t sum_memory_strdup;</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-uint64_t mask_nbseed ;</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-uint64_t mask_offset_seed; </span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-unsigned int nbits_nbseeds;</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) uint64_t mask_nbseed ;</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) uint64_t mask_offset_seed; </span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) unsigned int nbits_nbseeds;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> // macro to test if a variable is null (i.e., a malloc failed)</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> #define test_alloc( variable) { if(variable == NULL){ fprintf(stderr,"cannot allocate memory for variable %s, exit\n",#variable); exit(1); }}</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/thirdparty/kissreads/include/fragment_index.h</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/thirdparty/kissreads/include/fragment_index.h</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -49,10 +49,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> #include <couple.h></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-int number_of_starters;</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-hash_t seeds; // hash table seed -> (fragment id, position)</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-hash_t seeds_count;</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-couple * seed_table;</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) int number_of_starters;</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) hash_t seeds; // hash table seed -> (fragment id, position)</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) hash_t seeds_count;</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+__attribute__((__common__)) couple * seed_table;</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> 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.</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fix-bcalm-install.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">tests-2to3.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">spelling.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">gcc10.patch</span></pre>
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