diff --git a/README.md b/README.md index a3c511c..3b650a5 100644 --- a/README.md +++ b/README.md @@ -2,16 +2,39 @@ KMC = [![GitHub downloads](https://img.shields.io/github/downloads/refresh-bio/kmc/total.svg?style=flag&label=GitHub%20downloads)](https://github.com/refresh-bio/KMC/releases) [![Bioconda downloads](https://img.shields.io/conda/dn/bioconda/kmc.svg?style=flag&label=Bioconda%20downloads)](https://anaconda.org/bioconda/kmc) +[![GitHub Actions CI](../../actions/workflows/main.yml/badge.svg)](../../actions/workflows/main.yml) -KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files. -The homepage of the KMC project is http://sun.aei.polsl.pl/kmc +KMC is a disk-based program for counting k-mers from (possibly gzipped) FASTQ/FASTA files. +KMC is one of many projects developed by [REFRESH Bioinformatics Group](http://sun.aei.polsl.pl/REFRESH/). For accessing k-mers stored in database produced by KMC there is an API (kmc_api directory). Note that for KMC versions 0.x and 1.x dababase format differs from produced by KMC version 2.x. From version 2.2.0 API is unified for both formats and all new features/bug fixes are present only for 2.x branch (standalone API for older KMC version is not longer under development, so new version of API should be used even for databases produced by older KMC version). -Installation +Quick start += +#### Getting the executable +The simplest way to get the KMC is to download newest release for appropriate operating system from [KMC releases](https://github.com/refresh-bio/KMC/releases). +#### Counting the k-mers from a single fastq file +``` +./kmc -k27 input.fastq 27mers . +``` +The command above will count all the 27-mers occurring in ```input.fastq``` at least twice (configurable with ```-ci``` switch). +The result will be stored in a KMC database, which is split into two files: ```27mers.kmc_pre``` and ```27mers.kmc_suf```. +KMC will create hundreds of intermediate files. In the case of the above command, those will be created in the current working directory(the ```.``` at the end of the command). +It may be more convinient to use dedicated directory for KMC temporary files, for example: +``` +mkdir kmc_tmp # create directory for kmc temporary files +./kmc -k27 input.fastq 27mers kmc_tmp +``` +#### Create text dump from KMC database binary format +Having the k-mers counted it is possible to dump KMC binary database to textual form with ```kmc_tools```. +``` +./kmc_tools transform 27mers dump 27mers.txt +``` + +Installation details = The following libraries come with KMC in a binary (64-bit compiled for x86 platform) form. -If your system needs other binary formats, you should put the following libraries in kmer_counter/libs: +If your system needs other binary formats, you should put the following libraries in kmc_core/libs: * libbzip2 - for support for bzip2-compressed input FASTQ/FASTA files (http://www.bzip.org/) * zlib - for support for gzip-compressed input FASTQ/FASTA files (http://www.zlib.net/) @@ -39,12 +62,21 @@ To increase this number use following command before running KMC: Directory structure = - * bin - main directory of KMC (programs after compilation will be stored here) - * kmer_counter - source code of kmc program - * kmer_counter/libs - compiled binary versions of libraries used by KMC - * kmc_api - C++ source codes implementing API; must be used by any program that wants to process databases produced by kmc - * kmc_dump - source codes of kmc_dump program listing k-mers in databases produced by kmc + * bin - after compilation executables and libraries after compilation will be stored here + * include - after compilation header file to use kmc core through the C++ API will be stored here + * kmc_core - source code of kmc core library + * kmc_CLI - source code of kmc command line interface + * kmc_tools - source codes of kmc_tools program + * kmc_core/libs - libraries used by KMC + * kmc_api - C++ source codes implementing API to access KMC databases; must be used by any program that wants to process databases produced by kmc + * kmc_dump - source codes of kmc_dump program listing k-mers in databases produced by kmc (deprecated, use kmc_tools instead) * py_kmc_api - python wrapper for kmc API + * tests - tests files + +Use the KMC directly from code through the API += +It is possible to use the KMC directly from C++ code through. +Detailed API description is available at [wiki](https://github.com/refresh-bio/KMC/wiki/Use-the-KMC-directly-from-code-through-the-API) Python wrapper for KMC API = @@ -74,8 +106,7 @@ py_kmc_api\set_path.bat it will export apropriate file. The example of Python wrapper for KMC API is presented in file: py_kmc_api/py_kmc_dump.py -Detailed API describtion is avaiable at [wiki](https://github.com/refresh-bio/KMC/wiki/Python-wrapper-for-KMC-API) - +Detailed API description is available at [wiki](https://github.com/refresh-bio/KMC/wiki/Python-wrapper-for-KMC-API) Binaries = @@ -83,6 +114,8 @@ After compilation you will obtain two binaries: * bin/kmc - the main program for counting k-mer occurrences * bin/kmc_dump - the program listing k-mers in a database produced by kmc * bin/kmc_tools - the program allowing to manipulate kmc databases (set operations, transformations, etc.) +* bin/libkmc_core.a - compiled KMC code sources +* py_kmc_api.cpython-39-x86_64-linux-gnu.so - compiled python wrapper for KMC API License @@ -105,3 +138,9 @@ TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DI THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +## Citing +[Marek Kokot, Maciej DÅ‚ugosz, Sebastian Deorowicz, KMC 3: counting and manipulating k-mer statistics, Bioinformatics, Volume 33, Issue 17, 01 September 2017, Pages 2759–2761, https://doi.org/10.1093/bioinformatics/btx304](https://academic.oup.com/bioinformatics/article/33/17/2759/3796399) + +[Sebastian Deorowicz, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz, KMC 2: fast and resource-frugal k-mer counting, Bioinformatics, Volume 31, Issue 10, 15 May 2015, Pages 1569–1576, https://doi.org/10.1093/bioinformatics/btv022](https://academic.oup.com/bioinformatics/article/31/10/1569/177467) + +[Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. Disk-based k-mer counting on a PC. BMC Bioinformatics 14, 160 (2013). https://doi.org/10.1186/1471-2105-14-160](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-160) diff --git a/kmc_api/kmc_file.cpp b/kmc_api/kmc_file.cpp index e1a5889..62076ef 100644 --- a/kmc_api/kmc_file.cpp +++ b/kmc_api/kmc_file.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "mmer.h" diff --git a/kmc_api/kmc_file.h b/kmc_api/kmc_file.h index 4b7a6e0..7ed1917 100644 --- a/kmc_api/kmc_file.h +++ b/kmc_api/kmc_file.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KMC_FILE_H diff --git a/kmc_api/kmer_api.cpp b/kmc_api/kmer_api.cpp index 9958c97..88d9561 100644 --- a/kmc_api/kmer_api.cpp +++ b/kmc_api/kmer_api.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz and Agnieszka Debudaj-Grabysz - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "kmer_api.h" diff --git a/kmc_api/kmer_api.h b/kmc_api/kmer_api.h index 2081a88..d9d2ce0 100644 --- a/kmc_api/kmer_api.h +++ b/kmc_api/kmer_api.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz and Agnieszka Debudaj-Grabysz -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _KMER_API_H diff --git a/kmc_api/kmer_defs.h b/kmc_api/kmer_defs.h index c0a43e0..9a8cd85 100644 --- a/kmc_api/kmer_defs.h +++ b/kmc_api/kmer_defs.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz and Agnieszka Debudaj-Grabysz - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ @@ -14,8 +14,8 @@ #include -#define KMC_VER "3.1.1" -#define KMC_DATE "2019-05-19" +#define KMC_VER "3.2.0" +#define KMC_DATE "2021-12-23" #ifndef MIN #define MIN(x,y) ((x) < (y) ? (x) : (y)) diff --git a/kmc_api/mmer.cpp b/kmc_api/mmer.cpp index 5ef8c3c..322e695 100644 --- a/kmc_api/mmer.cpp +++ b/kmc_api/mmer.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "../kmc_api/mmer.h" diff --git a/kmc_api/mmer.h b/kmc_api/mmer.h index 35043c0..bedf874 100644 --- a/kmc_api/mmer.h +++ b/kmc_api/mmer.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _MMER_H diff --git a/kmc_api/stdafx.h b/kmc_api/stdafx.h deleted file mode 100644 index 1b64785..0000000 --- a/kmc_api/stdafx.h +++ /dev/null @@ -1,4 +0,0 @@ -#include -//#include -#include -using namespace std; diff --git a/kmc_core/bam_utils.h b/kmc_core/bam_utils.h index 2b2f643..bd9bb95 100644 --- a/kmc_core/bam_utils.h +++ b/kmc_core/bam_utils.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _BAM_UTILS_H diff --git a/kmc_core/binary_reader.h b/kmc_core/binary_reader.h index cfa0e31..9f157f2 100644 --- a/kmc_core/binary_reader.h +++ b/kmc_core/binary_reader.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _BINARY_READER_H diff --git a/kmc_core/bkb_merger.h b/kmc_core/bkb_merger.h index d96af68..81b16c7 100644 --- a/kmc_core/bkb_merger.h +++ b/kmc_core/bkb_merger.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _HBH_MERGER_H diff --git a/kmc_core/bkb_reader.cpp b/kmc_core/bkb_reader.cpp index 510d93f..3ec5ad4 100644 --- a/kmc_core/bkb_reader.cpp +++ b/kmc_core/bkb_reader.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "bkb_reader.h" diff --git a/kmc_core/bkb_reader.h b/kmc_core/bkb_reader.h index 78734b0..07e32c8 100644 --- a/kmc_core/bkb_reader.h +++ b/kmc_core/bkb_reader.h @@ -5,8 +5,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _BKB_READER_H_ diff --git a/kmc_core/bkb_sorter.h b/kmc_core/bkb_sorter.h index db2a457..86b090d 100644 --- a/kmc_core/bkb_sorter.h +++ b/kmc_core/bkb_sorter.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _BKB_SORTER_H diff --git a/kmc_core/bkb_subbin.h b/kmc_core/bkb_subbin.h index 1f0f171..1182a05 100644 --- a/kmc_core/bkb_subbin.h +++ b/kmc_core/bkb_subbin.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _BKB_SUBBIN_H diff --git a/kmc_core/bkb_uncompactor.h b/kmc_core/bkb_uncompactor.h index 746ebb9..0960e99 100644 --- a/kmc_core/bkb_uncompactor.h +++ b/kmc_core/bkb_uncompactor.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _BKB_UNCOMPACTOR_H diff --git a/kmc_core/bkb_writer.cpp b/kmc_core/bkb_writer.cpp index 70d82bc..eec775b 100644 --- a/kmc_core/bkb_writer.cpp +++ b/kmc_core/bkb_writer.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "bkb_writer.h" diff --git a/kmc_core/bkb_writer.h b/kmc_core/bkb_writer.h index 863ecb3..5dc78c7 100644 --- a/kmc_core/bkb_writer.h +++ b/kmc_core/bkb_writer.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _BKB_WRITER_H diff --git a/kmc_core/cpu_info.cpp b/kmc_core/cpu_info.cpp index 8df4f8c..16a4311 100644 --- a/kmc_core/cpu_info.cpp +++ b/kmc_core/cpu_info.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "cpu_info.h" diff --git a/kmc_core/cpu_info.h b/kmc_core/cpu_info.h index 0767c59..40c7d44 100644 --- a/kmc_core/cpu_info.h +++ b/kmc_core/cpu_info.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _CPU_INFO_ diff --git a/kmc_core/defs.h b/kmc_core/defs.h index 2a3af4b..69eab6e 100644 --- a/kmc_core/defs.h +++ b/kmc_core/defs.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _DEFS_H @@ -13,8 +13,8 @@ #include -#define KMC_VER "3.1.1" -#define KMC_DATE "2019-05-19" +#define KMC_VER "3.2.0" +#define KMC_DATE "2021-12-23" #define _CRT_SECURE_NO_WARNINGS diff --git a/kmc_core/fastq_reader.cpp b/kmc_core/fastq_reader.cpp index 294e570..c06138b 100644 --- a/kmc_core/fastq_reader.cpp +++ b/kmc_core/fastq_reader.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include diff --git a/kmc_core/fastq_reader.h b/kmc_core/fastq_reader.h index 20bd4fd..5d7e138 100644 --- a/kmc_core/fastq_reader.h +++ b/kmc_core/fastq_reader.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _FASTQ_READER_H diff --git a/kmc_core/first_dispatch.h b/kmc_core/first_dispatch.h index 678aa10..15c9a60 100644 --- a/kmc_core/first_dispatch.h +++ b/kmc_core/first_dispatch.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _FIRST_DISPATCH_H #define _FIRST_DISPATCH_H @@ -85,13 +85,13 @@ class CRangeQueue return true; } return false; - //TODO: dodaæ obs³ugê badania poprawnych danych, tzn przynajmniej jednego rekordu + //TODO: doda� obs�ug� badania poprawnych danych, tzn przynajmniej jednego rekordu } void reset_indices() { cur_idx = 0; - done = false; //TODO: dodaæ obs³ugê badania poprawnych danych + done = false; //TODO: doda� obs�ug� badania poprawnych danych } }; diff --git a/kmc_core/intr_copy.h b/kmc_core/intr_copy.h index b7a5c84..84d889c 100644 --- a/kmc_core/intr_copy.h +++ b/kmc_core/intr_copy.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _INTR_COPY_H diff --git a/kmc_core/kb_collector.cpp b/kmc_core/kb_collector.cpp index dd6d009..9e0ddf6 100644 --- a/kmc_core/kb_collector.cpp +++ b/kmc_core/kb_collector.cpp @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #include "kb_collector.h" diff --git a/kmc_core/kb_collector.h b/kmc_core/kb_collector.h index cd1592d..bc66c78 100644 --- a/kmc_core/kb_collector.h +++ b/kmc_core/kb_collector.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KB_COLLECTOR_H diff --git a/kmc_core/kb_completer.cpp b/kmc_core/kb_completer.cpp index 3f24167..3edbe3a 100644 --- a/kmc_core/kb_completer.cpp +++ b/kmc_core/kb_completer.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include #include diff --git a/kmc_core/kb_completer.h b/kmc_core/kb_completer.h index e4e8b12..8d3733e 100644 --- a/kmc_core/kb_completer.h +++ b/kmc_core/kb_completer.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KB_COMPLETER_H #define _KB_COMPLETER_H diff --git a/kmc_core/kb_reader.h b/kmc_core/kb_reader.h index 6d03348..f785340 100644 --- a/kmc_core/kb_reader.h +++ b/kmc_core/kb_reader.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KB_READER_H diff --git a/kmc_core/kb_sorter.h b/kmc_core/kb_sorter.h index bc6440d..8bb0ef7 100644 --- a/kmc_core/kb_sorter.h +++ b/kmc_core/kb_sorter.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KB_SORTER_H diff --git a/kmc_core/kb_storer.cpp b/kmc_core/kb_storer.cpp index 8a5e420..51c1982 100644 --- a/kmc_core/kb_storer.cpp +++ b/kmc_core/kb_storer.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include #include diff --git a/kmc_core/kb_storer.h b/kmc_core/kb_storer.h index 192676e..30322c8 100644 --- a/kmc_core/kb_storer.h +++ b/kmc_core/kb_storer.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KB_STORER_H diff --git a/kmc_core/kmc.h b/kmc_core/kmc.h index f32f7ca..ac5e97a 100644 --- a/kmc_core/kmc.h +++ b/kmc_core/kmc.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KMC_H diff --git a/kmc_core/kmc_runner.cpp b/kmc_core/kmc_runner.cpp index 710226d..a1903c6 100644 --- a/kmc_core/kmc_runner.cpp +++ b/kmc_core/kmc_runner.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "kmc_runner.h" diff --git a/kmc_core/kmc_runner.h b/kmc_core/kmc_runner.h index 434f896..4528f1b 100644 --- a/kmc_core/kmc_runner.h +++ b/kmc_core/kmc_runner.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KMC_RUNNER diff --git a/kmc_core/kmer.cpp b/kmc_core/kmer.cpp index c491bdb..151f940 100644 --- a/kmc_core/kmer.cpp +++ b/kmc_core/kmer.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "defs.h" diff --git a/kmc_core/kmer.h b/kmc_core/kmer.h index c4589c3..b7fc9b8 100644 --- a/kmc_core/kmer.h +++ b/kmc_core/kmer.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KMER_H diff --git a/kmc_core/kxmer_set.h b/kmc_core/kxmer_set.h index 7753779..1a58aa5 100644 --- a/kmc_core/kxmer_set.h +++ b/kmc_core/kxmer_set.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KXMER_SET_ #define _KXMER_SET_ diff --git a/kmc_core/mem_disk_file.cpp b/kmc_core/mem_disk_file.cpp index de3cda3..9ea6dcf 100644 --- a/kmc_core/mem_disk_file.cpp +++ b/kmc_core/mem_disk_file.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "mem_disk_file.h" diff --git a/kmc_core/mem_disk_file.h b/kmc_core/mem_disk_file.h index 35272ca..db99e24 100644 --- a/kmc_core/mem_disk_file.h +++ b/kmc_core/mem_disk_file.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _MEM_DISK_FILE_H diff --git a/kmc_core/meta_oper.h b/kmc_core/meta_oper.h index 990680a..f3ee277 100644 --- a/kmc_core/meta_oper.h +++ b/kmc_core/meta_oper.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _META_OPER_H diff --git a/kmc_core/params.h b/kmc_core/params.h index 406201b..00c3deb 100644 --- a/kmc_core/params.h +++ b/kmc_core/params.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _PARAMS_H diff --git a/kmc_core/percent_progress.h b/kmc_core/percent_progress.h index 3d12ebd..f190803 100644 --- a/kmc_core/percent_progress.h +++ b/kmc_core/percent_progress.h @@ -5,7 +5,7 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot Version: 3.0.0 -Date : 2019-05-19 +Date : 2021-12-23 */ #ifndef _PERCENT_PROGRESS_H diff --git a/kmc_core/queues.h b/kmc_core/queues.h index 3421eef..3abd38d 100644 --- a/kmc_core/queues.h +++ b/kmc_core/queues.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _QUEUES_H diff --git a/kmc_core/radix.h b/kmc_core/radix.h index b0dec5c..367c6b1 100644 --- a/kmc_core/radix.h +++ b/kmc_core/radix.h @@ -5,7 +5,7 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot Version: 3.1. -Date : 2019-05-19 +Date : 2021-12-23 */ #ifndef _RADIX_H #define _RADIX_H diff --git a/kmc_core/raduls.h b/kmc_core/raduls.h index f22d8a2..8283a52 100644 --- a/kmc_core/raduls.h +++ b/kmc_core/raduls.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef RADULS_H diff --git a/kmc_core/raduls_avx.cpp b/kmc_core/raduls_avx.cpp index e9009ce..1844ad0 100644 --- a/kmc_core/raduls_avx.cpp +++ b/kmc_core/raduls_avx.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "raduls_impl.h" diff --git a/kmc_core/raduls_avx2.cpp b/kmc_core/raduls_avx2.cpp index e9009ce..1844ad0 100644 --- a/kmc_core/raduls_avx2.cpp +++ b/kmc_core/raduls_avx2.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "raduls_impl.h" diff --git a/kmc_core/raduls_impl.h b/kmc_core/raduls_impl.h index 01b851e..835a3c9 100644 --- a/kmc_core/raduls_impl.h +++ b/kmc_core/raduls_impl.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _RADULS_IMPL_H diff --git a/kmc_core/raduls_sse2.cpp b/kmc_core/raduls_sse2.cpp index e9009ce..1844ad0 100644 --- a/kmc_core/raduls_sse2.cpp +++ b/kmc_core/raduls_sse2.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "raduls_impl.h" diff --git a/kmc_core/raduls_sse41.cpp b/kmc_core/raduls_sse41.cpp index e9009ce..1844ad0 100644 --- a/kmc_core/raduls_sse41.cpp +++ b/kmc_core/raduls_sse41.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "raduls_impl.h" diff --git a/kmc_core/rev_byte.cpp b/kmc_core/rev_byte.cpp index e6dfa5c..93942f7 100644 --- a/kmc_core/rev_byte.cpp +++ b/kmc_core/rev_byte.cpp @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "rev_byte.h" diff --git a/kmc_core/rev_byte.h b/kmc_core/rev_byte.h index 44e9a4f..df965a8 100644 --- a/kmc_core/rev_byte.h +++ b/kmc_core/rev_byte.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _REV_BYTE_H diff --git a/kmc_core/s_mapper.h b/kmc_core/s_mapper.h index ad6128f..27d4a9b 100644 --- a/kmc_core/s_mapper.h +++ b/kmc_core/s_mapper.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _S_MAPPER_H diff --git a/kmc_core/small_k_buf.h b/kmc_core/small_k_buf.h index 51fd2ef..2a9474e 100644 --- a/kmc_core/small_k_buf.h +++ b/kmc_core/small_k_buf.h @@ -4,7 +4,7 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 + Version: 3.2.0 Date : 2017-01-28 */ diff --git a/kmc_core/small_sort.h b/kmc_core/small_sort.h index 6c997df..9becde5 100644 --- a/kmc_core/small_sort.h +++ b/kmc_core/small_sort.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _SMALL_SORT_H #define _SMALL_SORT_H diff --git a/kmc_core/splitter.cpp b/kmc_core/splitter.cpp index 1630ce7..3f46c90 100644 --- a/kmc_core/splitter.cpp +++ b/kmc_core/splitter.cpp @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #include "splitter.h" diff --git a/kmc_core/splitter.h b/kmc_core/splitter.h index c1b187c..f544d78 100644 --- a/kmc_core/splitter.h +++ b/kmc_core/splitter.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _SPLITTER_H diff --git a/kmc_core/timer.cpp b/kmc_core/timer.cpp index 7f2b681..7c024dd 100644 --- a/kmc_core/timer.cpp +++ b/kmc_core/timer.cpp @@ -5,8 +5,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc The source codes are based on codes written by Dennis and published: http://allmybrain.com/2008/06/10/timing-cc-code-on-linux/ -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifdef _WIN32 diff --git a/kmc_core/timer.h b/kmc_core/timer.h index a9203e5..e2380cf 100644 --- a/kmc_core/timer.h +++ b/kmc_core/timer.h @@ -5,8 +5,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc The source codes are based on codes written by Dennis and published: http://allmybrain.com/2008/06/10/timing-cc-code-on-linux/ -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _TIMER_H diff --git a/kmc_core/tmp_files_owner.h b/kmc_core/tmp_files_owner.h index 17ec7f8..15ad988 100644 --- a/kmc_core/tmp_files_owner.h +++ b/kmc_core/tmp_files_owner.h @@ -4,8 +4,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _TMP_FILES_OWNER_H diff --git a/kmc_dump/kmc_dump.cpp b/kmc_dump/kmc_dump.cpp index 86fc3a6..c73f479 100644 --- a/kmc_dump/kmc_dump.cpp +++ b/kmc_dump/kmc_dump.cpp @@ -7,8 +7,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include diff --git a/kmc_dump/nc_utils.cpp b/kmc_dump/nc_utils.cpp index 51e923e..c205486 100644 --- a/kmc_dump/nc_utils.cpp +++ b/kmc_dump/nc_utils.cpp @@ -7,8 +7,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "nc_utils.h" diff --git a/kmc_dump/nc_utils.h b/kmc_dump/nc_utils.h index a682645..dbfc5e1 100644 --- a/kmc_dump/nc_utils.h +++ b/kmc_dump/nc_utils.h @@ -7,8 +7,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include diff --git a/kmc_dump_sample/kmc_dump_sample.cpp b/kmc_dump_sample/kmc_dump_sample.cpp index 8c409bf..0430152 100644 --- a/kmc_dump_sample/kmc_dump_sample.cpp +++ b/kmc_dump_sample/kmc_dump_sample.cpp @@ -7,8 +7,8 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include diff --git a/kmc_tools/bundle.h b/kmc_tools/bundle.h index 9be492a..ef9cb60 100644 --- a/kmc_tools/bundle.h +++ b/kmc_tools/bundle.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _BUNDLE_H diff --git a/kmc_tools/check_kmer.h b/kmc_tools/check_kmer.h index fe1976d..aac1284 100644 --- a/kmc_tools/check_kmer.h +++ b/kmc_tools/check_kmer.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _CHECK_KMER_H diff --git a/kmc_tools/config.h b/kmc_tools/config.h index d023eac..eb08898 100644 --- a/kmc_tools/config.h +++ b/kmc_tools/config.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _CONFIG_H diff --git a/kmc_tools/db_writer.h b/kmc_tools/db_writer.h index 71e70da..299e8ad 100644 --- a/kmc_tools/db_writer.h +++ b/kmc_tools/db_writer.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _DB_WRITER_H diff --git a/kmc_tools/defs.h b/kmc_tools/defs.h index 2433b67..2d2763b 100644 --- a/kmc_tools/defs.h +++ b/kmc_tools/defs.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _DEFS_H @@ -32,8 +32,8 @@ using uchar = unsigned char; //#define ENABLE_DEBUG //#define ENABLE_LOGGER -#define KMC_VER "3.1.1" -#define KMC_DATE "2019-05-19" +#define KMC_VER "3.2.0" +#define KMC_DATE "2021-12-23" #define DEFAULT_CIRCULAL_QUEUE_CAPACITY (4) diff --git a/kmc_tools/dump_writer.h b/kmc_tools/dump_writer.h index 52e5546..9e77ec6 100644 --- a/kmc_tools/dump_writer.h +++ b/kmc_tools/dump_writer.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _DUMP_WRITER_H diff --git a/kmc_tools/expression_node.h b/kmc_tools/expression_node.h index 921628f..d8f770c 100644 --- a/kmc_tools/expression_node.h +++ b/kmc_tools/expression_node.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _EXPRESSION_NODE_H diff --git a/kmc_tools/fastq_filter.cpp b/kmc_tools/fastq_filter.cpp index be552c0..3fd2b4d 100644 --- a/kmc_tools/fastq_filter.cpp +++ b/kmc_tools/fastq_filter.cpp @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #include "fastq_filter.h" diff --git a/kmc_tools/fastq_filter.h b/kmc_tools/fastq_filter.h index 4372ed0..f972f33 100644 --- a/kmc_tools/fastq_filter.h +++ b/kmc_tools/fastq_filter.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _FASTQ_FILTER_H diff --git a/kmc_tools/fastq_reader.cpp b/kmc_tools/fastq_reader.cpp index 5694469..3d869e2 100644 --- a/kmc_tools/fastq_reader.cpp +++ b/kmc_tools/fastq_reader.cpp @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include diff --git a/kmc_tools/fastq_reader.h b/kmc_tools/fastq_reader.h index 1bcb42d..ef9bb69 100644 --- a/kmc_tools/fastq_reader.h +++ b/kmc_tools/fastq_reader.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _FASTQ_READER_H diff --git a/kmc_tools/fastq_writer.cpp b/kmc_tools/fastq_writer.cpp index 438724c..825475f 100644 --- a/kmc_tools/fastq_writer.cpp +++ b/kmc_tools/fastq_writer.cpp @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "fastq_writer.h" diff --git a/kmc_tools/fastq_writer.h b/kmc_tools/fastq_writer.h index 5de0186..0cae2ed 100644 --- a/kmc_tools/fastq_writer.h +++ b/kmc_tools/fastq_writer.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _FASTQ_WRITER_H diff --git a/kmc_tools/histogram_writer.h b/kmc_tools/histogram_writer.h index 9601d6a..91385a6 100644 --- a/kmc_tools/histogram_writer.h +++ b/kmc_tools/histogram_writer.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _HISTOGRAM_WRITER_H diff --git a/kmc_tools/kff_db_writer.h b/kmc_tools/kff_db_writer.h index 1310275..234f685 100644 --- a/kmc_tools/kff_db_writer.h +++ b/kmc_tools/kff_db_writer.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ //TODO KFF: consider separate thread for writing linke in kmc1 db writer diff --git a/kmc_tools/kff_kmc2_reader_utils.h b/kmc_tools/kff_kmc2_reader_utils.h index 6805da8..205e290 100644 --- a/kmc_tools/kff_kmc2_reader_utils.h +++ b/kmc_tools/kff_kmc2_reader_utils.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _KFF_KMC2_UTILS_H diff --git a/kmc_tools/kff_random_access.h b/kmc_tools/kff_random_access.h index 58448f9..cabd4cc 100644 --- a/kmc_tools/kff_random_access.h +++ b/kmc_tools/kff_random_access.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KFF_RANDOM_ACCESS_H diff --git a/kmc_tools/kmc1_db_reader.h b/kmc_tools/kmc1_db_reader.h index d65120f..41f6736 100644 --- a/kmc_tools/kmc1_db_reader.h +++ b/kmc_tools/kmc1_db_reader.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _KMC1_DB_READER_H diff --git a/kmc_tools/kmc1_db_writer.h b/kmc_tools/kmc1_db_writer.h index 6dfc97d..036366b 100644 --- a/kmc_tools/kmc1_db_writer.h +++ b/kmc_tools/kmc1_db_writer.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _KMC1_DB_WRITER_H diff --git a/kmc_tools/kmc2_db_reader.h b/kmc_tools/kmc2_db_reader.h index 065dc33..f967ba4 100644 --- a/kmc_tools/kmc2_db_reader.h +++ b/kmc_tools/kmc2_db_reader.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _KMC2_DB_READER_H diff --git a/kmc_tools/kmc_tools.cpp b/kmc_tools/kmc_tools.cpp index 614eeea..597351d 100644 --- a/kmc_tools/kmc_tools.cpp +++ b/kmc_tools/kmc_tools.cpp @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include diff --git a/kmc_tools/kmer.h b/kmc_tools/kmer.h index 9a573d9..50b26ae 100644 --- a/kmc_tools/kmer.h +++ b/kmc_tools/kmer.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _KMER_H diff --git a/kmc_tools/kmer_file_header.cpp b/kmc_tools/kmer_file_header.cpp index 0c43798..55bbeb2 100644 --- a/kmc_tools/kmer_file_header.cpp +++ b/kmc_tools/kmer_file_header.cpp @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "kmer_file_header.h" diff --git a/kmc_tools/kmer_file_header.h b/kmc_tools/kmer_file_header.h index b7256ed..1b8d1d8 100644 --- a/kmc_tools/kmer_file_header.h +++ b/kmc_tools/kmer_file_header.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _KMER_FILE_HEADER_H diff --git a/kmc_tools/meta_oper.h b/kmc_tools/meta_oper.h index 987b12b..f7e3174 100644 --- a/kmc_tools/meta_oper.h +++ b/kmc_tools/meta_oper.h @@ -4,8 +4,8 @@ The homepage of the KMC project is http://sun.aei.polsl.pl/kmc Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot -Version: 3.1.1 -Date : 2019-05-19 +Version: 3.2.0 +Date : 2021-12-23 */ #ifndef _META_OPER_H diff --git a/kmc_tools/nc_utils.cpp b/kmc_tools/nc_utils.cpp index 945efd8..67829d6 100644 --- a/kmc_tools/nc_utils.cpp +++ b/kmc_tools/nc_utils.cpp @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "nc_utils.h" diff --git a/kmc_tools/nc_utils.h b/kmc_tools/nc_utils.h index 6df7e55..7aaca19 100644 --- a/kmc_tools/nc_utils.h +++ b/kmc_tools/nc_utils.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include diff --git a/kmc_tools/operations.h b/kmc_tools/operations.h index d8721e0..284955a 100644 --- a/kmc_tools/operations.h +++ b/kmc_tools/operations.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _OPERATIONS_H diff --git a/kmc_tools/output_parser.h b/kmc_tools/output_parser.h index 46bbfda..08a7ed9 100644 --- a/kmc_tools/output_parser.h +++ b/kmc_tools/output_parser.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _OUTPUT_PARSER_H diff --git a/kmc_tools/parameters_parser.cpp b/kmc_tools/parameters_parser.cpp index b05130d..468abd6 100644 --- a/kmc_tools/parameters_parser.cpp +++ b/kmc_tools/parameters_parser.cpp @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "parameters_parser.h" diff --git a/kmc_tools/parameters_parser.h b/kmc_tools/parameters_parser.h index 7fa5146..d03adca 100644 --- a/kmc_tools/parameters_parser.h +++ b/kmc_tools/parameters_parser.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _PARAMETERS_PARSER_H diff --git a/kmc_tools/parser.cpp b/kmc_tools/parser.cpp index bd1743e..7324c93 100644 --- a/kmc_tools/parser.cpp +++ b/kmc_tools/parser.cpp @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "parser.h" diff --git a/kmc_tools/parser.h b/kmc_tools/parser.h index 0d9992b..1d57b74 100644 --- a/kmc_tools/parser.h +++ b/kmc_tools/parser.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _PARSER_H diff --git a/kmc_tools/percent_progress.cpp b/kmc_tools/percent_progress.cpp index 7b2a017..d2a45aa 100644 --- a/kmc_tools/percent_progress.cpp +++ b/kmc_tools/percent_progress.cpp @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #include "percent_progress.h" diff --git a/kmc_tools/percent_progress.h b/kmc_tools/percent_progress.h index 15d0313..cdee9e9 100644 --- a/kmc_tools/percent_progress.h +++ b/kmc_tools/percent_progress.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _PERCENT_PROGRESS_H diff --git a/kmc_tools/queues.h b/kmc_tools/queues.h index cd64ee3..4444914 100644 --- a/kmc_tools/queues.h +++ b/kmc_tools/queues.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _QUEUES_H_ diff --git a/kmc_tools/thread_watch.h b/kmc_tools/thread_watch.h index e65bcb8..29472b2 100644 --- a/kmc_tools/thread_watch.h +++ b/kmc_tools/thread_watch.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _THREAD_WATCH_H diff --git a/kmc_tools/timer.h b/kmc_tools/timer.h index b7d96f6..9f1b5e8 100644 --- a/kmc_tools/timer.h +++ b/kmc_tools/timer.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _TIMER_H diff --git a/kmc_tools/tokenizer.cpp b/kmc_tools/tokenizer.cpp index be60fed..c75da1a 100644 --- a/kmc_tools/tokenizer.cpp +++ b/kmc_tools/tokenizer.cpp @@ -4,7 +4,7 @@ Authors: Marek Kokot - Version: 3.1.1 + Version: 3.2.0 Date : 2017-01-28 */ diff --git a/kmc_tools/tokenizer.h b/kmc_tools/tokenizer.h index 1c07596..b1e0cdc 100644 --- a/kmc_tools/tokenizer.h +++ b/kmc_tools/tokenizer.h @@ -4,8 +4,8 @@ Authors: Marek Kokot - Version: 3.1.1 - Date : 2019-05-19 + Version: 3.2.0 + Date : 2021-12-23 */ #ifndef _TOKENIZER_H diff --git a/py_kmc_api/py_kmc_dump.py b/py_kmc_api/py_kmc_dump.py index a14e87e..6fda672 100644 --- a/py_kmc_api/py_kmc_dump.py +++ b/py_kmc_api/py_kmc_dump.py @@ -4,8 +4,8 @@ import argparse import textwrap -VER = "3.1.1" -DATE = "2019-05-19" +VER = "3.2.0" +DATE = "2021-12-23" def GeneralHelp(): print('KMC dump ver. {} ({})'.format(VER, DATE)) diff --git a/tests/py_kmc_api/test_py_kmc_file.py b/tests/py_kmc_api/test_py_kmc_file.py index 6bf4516..7915e64 100755 --- a/tests/py_kmc_api/test_py_kmc_file.py +++ b/tests/py_kmc_api/test_py_kmc_file.py @@ -21,7 +21,7 @@ def create_kmc_db(): Set up tests and clean up after. ''' kmer_len = 17 - memory = 1 #GB + memory = 2 #GB cutoff_min = 1 sig_len = 9 reads_src = 'input.fastq' @@ -120,6 +120,7 @@ def _run_kmc(cutoff_min, kmer_len, memory, sig_len, reads_src): if init_sys_path.is_mac(): resource.setrlimit(resource.RLIMIT_NOFILE, (2048, 2048)) + subprocess.call([kmc_path, '-ci{}'.format(cutoff_min), '-k{}'.format(kmer_len), @@ -129,8 +130,7 @@ def _run_kmc(cutoff_min, kmer_len, memory, sig_len, reads_src): 'kmc_db', '.' ]) - - + def _open_for_listing(): ''' Open kmc database for listing and check if opened sucessfully. '''