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* dev: (123 commits) update changelog and readme fix single-end inpipe error kill input process when sdbg_build meets errors update megahit script: delete in pipe files when builder report errors reset default k to k-step 20, look good enough update megahit script fix local assembly when read length > 200 rename toolkits -> toolkit trim at N when reading reads add bz2 support (via mkfifo) add k-list support; try spades' list implement sequence package's reserve functions put assemble, local_assemble and iter into one program megahit_asm_core update megahit script logging fix min final standalone miscalculation add megahit toolkit assembler's min standalone length set to 3*k_max-1 formatted by astyle bug fixes && makefile update re-add --input-cmd option output to final.contigs.fa when --no-local is checked (faster) ... Conflicts: megahit
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| /* | ||
| * MEGAHIT | ||
| * Copyright (C) 2014 - 2015 The University of Hong Kong | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
|
|
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| /* contact: Dinghua Li <[email protected]> */ | ||
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| #include <stdio.h> | ||
| #include <stdlib.h> | ||
| #include <string.h> | ||
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|
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| #include "utils.h" | ||
|
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| int main_assemble(int argc, char** argv); | ||
| int main_local(int argc, char **argv); | ||
| int main_iterate(int argc, char **argv); | ||
|
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| void show_help(const char *program_name) { | ||
| fprintf(stderr, "Usage: %s <sub_program> [sub options]\n" | ||
| " sub-programs:\n" | ||
| " assemble assemble from SdBG\n" | ||
| " local local asssembly\n" | ||
| " iterate extract iterative edges\n", | ||
| program_name); | ||
| } | ||
|
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| AutoMaxRssRecorder recorder; | ||
|
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| int main(int argc, char **argv) { | ||
| if (argc < 2) { | ||
| show_help(argv[0]); | ||
| exit(1); | ||
| } | ||
|
|
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| if (strcmp(argv[1], "assemble") == 0) { | ||
| return main_assemble(argc - 1, argv + 1); | ||
| } else if (strcmp(argv[1], "local") == 0) { | ||
| return main_local(argc - 1 , argv + 1); | ||
| } else if (strcmp(argv[1], "iterate") == 0) { | ||
| return main_iterate(argc - 1, argv + 1); | ||
| } else { | ||
| show_help(argv[0]); | ||
| exit(1); | ||
| } | ||
|
|
||
| return 0; | ||
| } |
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