[med-svn] [kmc] 01/01: fix spelling
Sascha Steinbiss
sascha at steinbiss.name
Mon Dec 21 09:51:24 UTC 2015
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sascha-guest pushed a commit to branch master
in repository kmc.
commit ca8ca71b4ddb949039f4f049dc0b36ab872428a5
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Mon Dec 21 09:49:27 2015 +0000
fix spelling
this was already applied upstream, here's the patch for 2.3
---
debian/patches/series | 1 +
debian/patches/spelling | 193 ++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 194 insertions(+)
diff --git a/debian/patches/series b/debian/patches/series
index b9ba394..271460b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ use-shared-libs
hardening
0005-Add-static-library-target-to-makefile.patch
0007-Use-standard-compiler-environment-variables.patch
+spelling
diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644
index 0000000..a53f247
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,193 @@
+Description: fix spelling
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
+--- a/kmc_tools/config.h
++++ b/kmc_tools/config.h
+@@ -243,7 +243,7 @@
+ std::cout << " sort - sorts k-mers from database generated by KMC2.x\n";
+ std::cout << " reduce - exclude too rare and too frequent k-mers\n";
+ std::cout << " compact - remove counters (store only k-mers)\n";
+- std::cout << " histogram - histogram of k-mers occurences\n";
++ std::cout << " histogram - histogram of k-mers occurrences\n";
+ std::cout << " dump - dump k-mers and counters to text file\n";
+ std::cout << " more complex operations:\n";
+ std::cout << " complex - complex operations with a number of input databases\n";
+@@ -332,7 +332,7 @@
+ {}
+ void Display() const override
+ {
+- std::cout << "Complex operation allows to define operations for more than 2 input k-mers sets. Command-line syntax:\n";
++ std::cout << "Complex operation allows one to define operations for more than 2 input k-mers sets. Command-line syntax:\n";
+ std::cout << "kmc_tools complex <operations_definition_file>\n";
+ std::cout << " operations_definition_file - path to file which define input sets and operations. It is text file with following syntax:\n";
+ std::cout << " __________________________________________________________________ \n";
+@@ -355,7 +355,7 @@
+ std::cout << "out_db_path - path to output database\n";
+ std::cout << "ref_input - one of input1, input2, ..., inputN\n";
+ std::cout << "oper - one of {*,-,~,+}, which refers to {intersect, kmers_subtract, counters_subtract, union}\n";
+- std::cout << "operator * has the highest priority. Other operators has equals priorities. Order of operations can be changed with barenthesis\n";
++ std::cout << "operator * has the highest priority. Other operators has equals priorities. Order of operations can be changed with parentheses\n";
+ std::cout << "output_params are:\n";
+ std::cout << " -ci<value> - exclude k-mers occurring less than <value> times \n";
+ std::cout << " -cx<value> - exclude k-mers occurring more of than <value> times\n";
+@@ -547,4 +547,4 @@
+ #endif
+
+
+-// ***** EOF
+\ No newline at end of file
++// ***** EOF
+--- a/kmc_tools/libs/zlib.h
++++ b/kmc_tools/libs/zlib.h
+@@ -846,7 +846,7 @@
+ available input is skipped. No output is provided.
+
+ inflateSync searches for a 00 00 FF FF pattern in the compressed data.
+- All full flush points have this pattern, but not all occurences of this
++ All full flush points have this pattern, but not all occurrences of this
+ pattern are full flush points.
+
+ inflateSync returns Z_OK if a possible full flush point has been found,
+--- a/kmer_counter/bkb_sorter.h
++++ b/kmer_counter/bkb_sorter.h
+@@ -367,7 +367,7 @@
+ }
+
+ //----------------------------------------------------------------------------------
+-//Binary search position of first occurence of symbol 'symb' in [start_pos,end_pos). Offset defines which symbol in k+x-mer is taken.
++//Binary search position of first occurrence of symbol 'symb' in [start_pos,end_pos). Offset defines which symbol in k+x-mer is taken.
+ template <unsigned SIZE> uint64 CBigKmerBinSorter_Impl<CKmer<SIZE>, SIZE>::FindFirstSymbOccur(CBigKmerBinSorter<CKmer<SIZE>, SIZE> &ptr, uint64 start_pos, uint64 end_pos, uint32 offset, uchar symb)
+ {
+ uint32 kxmer_offset = (ptr.kmer_len + ptr.max_x - offset) * 2;
+--- a/kmer_counter/kb_sorter.h
++++ b/kmer_counter/kb_sorter.h
+@@ -830,7 +830,7 @@
+ }
+
+ //----------------------------------------------------------------------------------
+-//Binary search position of first occurence of symbol 'symb' in [start_pos,end_pos). Offset defines which symbol in k+x-mer is taken.
++//Binary search position of first occurrence of symbol 'symb' in [start_pos,end_pos). Offset defines which symbol in k+x-mer is taken.
+ template <unsigned SIZE> uint64 CKmerBinSorter_Impl<CKmer<SIZE>, SIZE>::FindFirstSymbOccur(CKmerBinSorter<CKmer<SIZE>, SIZE> &ptr, uint64 start_pos, uint64 end_pos, uint32 offset, uchar symb)
+ {
+ uint32 kxmer_offset = (ptr.kmer_len + ptr.max_x - offset) * 2;
+--- a/kmer_counter/s_mapper.h
++++ b/kmer_counter/s_mapper.h
+@@ -30,12 +30,12 @@
+
+ class Comp
+ {
+- uint32* signature_occurences;
++ uint32* signature_occurrences;
+ public:
+- Comp(uint32* _signature_occurences) : signature_occurences(_signature_occurences){}
++ Comp(uint32* _signature_occurrences) : signature_occurrences(_signature_occurrences){}
+ bool operator()(int i, int j)
+ {
+- return signature_occurences[i] > signature_occurences[j];
++ return signature_occurrences[i] > signature_occurrences[j];
+ }
+ };
+
+--- a/kmc_tools/kmc1_db_writer.h
++++ b/kmc_tools/kmc1_db_writer.h
+@@ -37,7 +37,7 @@
+ {
+ if (fwrite(buf, 1, size, kmc_suf) != size)
+ {
+- std::cout << "Error while writting to kmc_suf file\n";
++ std::cout << "Error while writing to kmc_suf file\n";
+ exit(1);
+ }
+ delete[] buf;
+@@ -78,9 +78,9 @@
+
+ void store_pre_buf();
+ void send_suf_buf_to_queue();
+- void start_writting();
++ void start_writing();
+ inline void add_kmer(CKmer<SIZE>& kmer, uint32 counter);
+- void finish_writting();
++ void finish_writing();
+
+ template<typename T> void write_header_part(T data);
+ void calc_lut_prefix_len();
+@@ -159,7 +159,7 @@
+ template<unsigned SIZE> bool CKMC1DbWriter<SIZE>::Process()
+ {
+
+- start_writting();
++ start_writing();
+
+ //Converts bundles to output buffers, sufix buffer is placed to another queue and write in separate thread (sufix_writer)
+ std::thread preparing_thread([this]{
+@@ -201,7 +201,7 @@
+ preparing_thread.join();
+ suf_buf_writing_thread.join();
+
+- finish_writting();
++ finish_writing();
+ return true;
+ }
+
+@@ -232,22 +232,22 @@
+ }
+
+ /*****************************************************************************************************************************/
+-template<unsigned SIZE> void CKMC1DbWriter<SIZE>::start_writting()
++template<unsigned SIZE> void CKMC1DbWriter<SIZE>::start_writing()
+ {
+ if (fwrite("KMCP", 1, 4, kmc_pre) != 4)
+ {
+- std::cout << "Error while writting starting KMCP marker";
++ std::cout << "Error while writing starting KMCP marker";
+ exit(1);
+ }
+ if (fwrite("KMCS", 1, 4, kmc_suf) != 4)
+ {
+- std::cout << "Error while writting starting KMCS marker";
++ std::cout << "Error while writing starting KMCS marker";
+ exit(1);
+ }
+ }
+
+ /*****************************************************************************************************************************/
+-template<unsigned SIZE> void CKMC1DbWriter<SIZE>::finish_writting()
++template<unsigned SIZE> void CKMC1DbWriter<SIZE>::finish_writing()
+ {
+ uint32 max_prefix = (1 << 2 * lut_prefix_len);
+ while (current_prefix < max_prefix - 1)
+@@ -284,12 +284,12 @@
+
+ if (fwrite("KMCP", 1, 4, kmc_pre) != 4)
+ {
+- std::cout << "Error while writting end KMCP marker";
++ std::cout << "Error while writing end KMCP marker";
+ exit(1);
+ }
+ if (fwrite("KMCS", 1, 4, kmc_suf) != 4)
+ {
+- std::cout << "Error while writting end KMCS marker";
++ std::cout << "Error while writing end KMCS marker";
+ exit(1);
+ }
+ fclose(kmc_pre);
+@@ -327,7 +327,7 @@
+ {
+ if (fwrite(pre_buff, sizeof(uint64), pre_pos, kmc_pre) != pre_pos)
+ {
+- std::cout << "Error while writting to kmc_pre file\n";
++ std::cout << "Error while writing to kmc_pre file\n";
+ exit(1);
+ }
+ pre_pos = 0;
+--- a/kmer_counter/radix.cpp
++++ b/kmer_counter/radix.cpp
+@@ -143,7 +143,7 @@
+ Satish, N., Kim, C., Chhugani, J., Nguyen, A.D., Lee, V.W., Kim, D., Dubey, P. (2010).
+ Fast Sort on CPUs and GPUs. A Case for Bandwidth Oblivious SIMD Sort.
+ Proc. of the 2010 Int. Conf. on Management of data, pp. 351�362.
+- The usage of software-managed buffers in the writting phase results in diminishing
++ The usage of software-managed buffers in the writing phase results in diminishing
+ the influence of irregular memory accesses. As the number of cache conflict misses
+ is reduced better efficiency is reached.*/
+ template<typename COUNTER_TYPE, typename INT_TYPE>
--
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