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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,5 @@ | ||
| ###0.2.0 | ||
| * Added bedgraph to bw functionality via bg2bw | ||
|
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| ###0.1.0 | ||
| * First release |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| 0.1.0 | ||
| 0.2.0 |
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| Original file line number | Diff line number | Diff line change |
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| /** LICENSE | ||
| * Copyright (c) 2016 Genome Research Ltd. | ||
| * | ||
| * Author: Cancer Genome Project [email protected] | ||
| * | ||
| * This file is part of cgpBigWig. | ||
| * | ||
| * cgpBigWig is free software: you can redistribute it and/or modify it under | ||
| * the terms of the GNU Affero 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 Affero General Public License for more | ||
| * details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| * | ||
| * 1. The usage of a range of years within a copyright statement contained within | ||
| * this distribution should be interpreted as being equivalent to a list of years | ||
| * including the first and last year specified and all consecutive years between | ||
| * them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- | ||
| * 2009, 2011-2012’ should be interpreted as being identical to a statement that | ||
| * reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright | ||
| * statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being | ||
| * identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, | ||
| * 2009, 2010, 2011, 2012’." | ||
| * | ||
| */ | ||
|
|
||
| #include <getopt.h> | ||
| #include <stdlib.h> | ||
| #include <stdio.h> | ||
| #include "bigWig.h" | ||
| #include "utils.h" | ||
| #include "dbg.h" | ||
|
|
||
| char *input_file = NULL; | ||
| char *out_file = "output.bw"; | ||
| char *chrlist = NULL; | ||
|
|
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| void print_usage (int exit_code){ | ||
| printf("Usage: bg2bw -i input.bed -c chrom.list -o output.bw\n"); | ||
| printf("bg2bw can be used to generate a bw file from a bedgraph file.\n\n"); | ||
| printf("-i --input [file] Path to the input [b|cr]am file.\n"); | ||
| printf("-o --outfile [file] Path to the output .bw file produced. [default:'%s']\n",out_file); | ||
| printf("-c --chromList [file] Path to chrom.list a .tsv where first two columns are contig name and length.\n\n"); | ||
| printf ("Other:\n"); | ||
| printf("-h --help Display this usage information.\n"); | ||
| printf("-v --version Prints the version number.\n\n"); | ||
|
|
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| exit(exit_code); | ||
| } | ||
|
|
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| void setup_options(int argc, char *argv[]){ | ||
| const struct option long_opts[] = | ||
| { | ||
| {"input", required_argument, 0, 'i'}, | ||
| {"outfile",required_argument, 0, 'o'}, | ||
| {"chromList",required_argument, 0, 'c'}, | ||
| {"help", no_argument, 0, 'h'}, | ||
| {"version", no_argument, 0, 'v'}, | ||
| { NULL, 0, NULL, 0} | ||
|
|
||
| }; //End of declaring opts | ||
|
|
||
| int index = 0; | ||
| int iarg = 0; | ||
|
|
||
| //Iterate through options | ||
| while((iarg = getopt_long(argc, argv, "c:i:o:hv",long_opts, &index)) != -1){ | ||
| switch(iarg){ | ||
| case 'i': | ||
| input_file = optarg; | ||
| if(check_exist(input_file) != 1){ | ||
| fprintf(stderr,"Input bed file %s does not appear to exist.\n",input_file); | ||
| print_usage(1); | ||
| } | ||
| break; | ||
|
|
||
| case 'c': | ||
| chrlist = optarg; | ||
| if(check_exist(chrlist) != 1){ | ||
| fprintf(stderr,"Input chrlist file %s does not appear to exist.\n",chrlist); | ||
| print_usage(1); | ||
| } | ||
| break; | ||
| case 'o': | ||
| out_file = optarg; | ||
| break; | ||
| case 'h': | ||
| print_usage (0); | ||
| break; | ||
| case 'v': | ||
| print_version (0); | ||
| break; | ||
| case '?': | ||
| print_usage (1); | ||
| break; | ||
| default: | ||
| print_usage (0); | ||
| }; // End of args switch statement | ||
|
|
||
| }//End of iteration through options | ||
|
|
||
| if(input_file==NULL){ | ||
| fprintf(stderr,"Required option -i|--input not defined.\n"); | ||
| print_usage(1); | ||
| } | ||
|
|
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| if(chrlist==NULL){ | ||
| fprintf(stderr,"Required option -c|--chrList not defined.\n"); | ||
| print_usage(1); | ||
| } | ||
|
|
||
| return; | ||
| } | ||
|
|
||
| chromList_t *parse_chrom_list(char *chrom_list_file){ | ||
| chromList_t *cl = NULL; | ||
| FILE *in = NULL; | ||
| char **contigs = NULL; | ||
| uint32_t *lengths = NULL; | ||
| int ln_count = line_count(chrom_list_file); | ||
| contigs = malloc(sizeof(char *) * ln_count); | ||
| check_mem(contigs); | ||
| lengths = malloc(sizeof(uint32_t *) * ln_count); | ||
| check_mem(lengths); | ||
| int chr_count = 0; | ||
| in = fopen(chrom_list_file,"r"); | ||
| check(in!=NULL,"Error opening chrom list file '%s' for reading.",chrom_list_file); | ||
| char line[2048]; | ||
| //Iterate through each line in the chromlist file | ||
| while(fgets(line, sizeof(line),in)){ | ||
| char *cntg = malloc(sizeof(char *) * 2048); | ||
| check_mem(cntg); | ||
| uint32_t len; | ||
| int no = sscanf(line,"%[^\t]\t%"SCNu32"\t",cntg,&len); | ||
| check(no==2,"Error extracting contig name and length from line %s.",line); | ||
| contigs[chr_count] = cntg; | ||
| lengths[chr_count] = len; | ||
| chr_count++; | ||
| } | ||
| check(chr_count==ln_count,"Error contigs found %d != line_count %d",chr_count,ln_count); | ||
| fclose(in); | ||
| cl = bwCreateChromList(contigs, lengths, chr_count); | ||
| check(cl!=NULL,"Error creating ChromList."); | ||
| return cl; | ||
|
|
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| error: | ||
| if(in) fclose(in); | ||
| if(contigs) free(contigs); | ||
| if(lengths) free(lengths); | ||
| return NULL; | ||
| } | ||
|
|
||
| int main(int argc, char *argv[]){ | ||
| setup_options(argc, argv); | ||
| FILE *in = NULL; | ||
| bigWigFile_t *fp = NULL; | ||
| char *ctg = NULL; | ||
| in = fopen(input_file,"r"); | ||
| check(in != NULL, "Error opeining input bed file '%s' to read.",input_file); | ||
|
|
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| //Read in the chromlist | ||
| int chk = bwInit(1<<17); | ||
| check(chk==0,"Received an error in bwInit: %d",chk); | ||
|
|
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| fp = bwOpen(out_file, NULL, "w"); | ||
| check(fp!=NULL,"Error opening output bw file '%s' for writing.",out_file); | ||
|
|
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| chk = bwCreateHdr(fp, 10); | ||
| check(chk==0,"Error creating bw header: %d.",chk); | ||
|
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| fp->cl = parse_chrom_list(chrlist); | ||
| check(fp->cl!=NULL,"Error parsing chrom list for contig information."); | ||
|
|
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| chk = bwWriteHdr(fp); | ||
| check(chk==0,"Error writing bw header: %d.",chk); | ||
|
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| char line[2048]; | ||
| int num = 0; | ||
| ctg = malloc(sizeof(char) * 2048); | ||
| uint32_t start; | ||
| uint32_t stop; | ||
| float res; | ||
| while(fgets(line,sizeof(line),in)){ | ||
| num = sscanf(line,"%[^\t]\t%"SCNu32"\t%"SCNu32"\t%f\n",ctg,&start,&stop,&res); | ||
| check(num==4,"Error parsing bed line '%s' to bw format.",line); | ||
| chk = bwAddIntervals(fp, &ctg, &start, &stop, &res, 1); | ||
| check(chk==0,"Error encountered adding bed line '%s' to bw file: %d.",line,chk); | ||
| } | ||
|
|
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| free(ctg); | ||
| fclose(in); | ||
| bwClose(fp); | ||
| bwCleanup(); | ||
| return 0; | ||
| error: | ||
| if(fp) bwClose(fp); | ||
| bwCleanup(); | ||
| if(ctg) free(ctg); | ||
| if(in) fclose(in); | ||
| return 1; | ||
| } | ||
|
|
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| Original file line number | Diff line number | Diff line change |
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| #!/bin/bash | ||
|
|
||
| ########## LICENSE ########## | ||
| # Copyright (c) 2016 Genome Research Ltd. | ||
| # | ||
| # Author: Cancer Genome Project [email protected] | ||
| # | ||
| # This file is part of cgpBigWig. | ||
| # | ||
| # cgpBigWig is free software: you can redistribute it and/or modify it under | ||
| # the terms of the GNU Affero 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 Affero General Public License for more | ||
| # details. | ||
| # | ||
| # You should have received a copy of the GNU Affero General Public License | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| # | ||
| # 1. The usage of a range of years within a copyright statement contained within | ||
| # this distribution should be interpreted as being equivalent to a list of years | ||
| # including the first and last year specified and all consecutive years between | ||
| # them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- | ||
| # 2009, 2011-2012’ should be interpreted as being identical to a statement that | ||
| # reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright | ||
| # statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being | ||
| # identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, | ||
| # 2009, 2010, 2011, 2012’." | ||
| # | ||
| ########################### | ||
|
|
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| ../bin/bg2bw -i ../test_data/volvox-sorted.coverage.expected.bed -o ../test_data/bg2bw.got.bw -c ../test_data/volvox.fa.fai; | ||
| if [ "$?" != "0" ]; | ||
| then | ||
| echo "ERROR in "$0": Running bw2bg" | ||
| echo "------" | ||
| rm -f ../test_data/bg2bw.got.bw | ||
| exit 1 | ||
| fi | ||
|
|
||
| ../bin/bwcat -i ../test_data/bg2bw.got.bw > ../test_data/bg2bw.got.bed; | ||
| if [ "$?" != "0" ]; | ||
| then | ||
| echo "ERROR in "$0": Running bwcat" | ||
| echo "------" | ||
| rm -f ../test_data/bg2bw.got.bw ../test_data/bg2bw.got.bed | ||
| exit 1 | ||
| fi | ||
|
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| ../bin/bwcat -i ../test_data/volvox-sorted.coverage.expected.bw > ../test_data/volvox-sorted.coverage.expected.out; | ||
| if [ "$?" != "0" ]; | ||
| then | ||
| echo "ERROR in "$0": Running bwcat" | ||
| echo "------" | ||
| rm -f ../test_data/bg2bw.got.bw ../test_data/bg2bw.got.bed ../test_data/volvox-sorted.coverage.expected.out | ||
| exit 1 | ||
| fi | ||
|
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|
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|
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| diff ../test_data/bg2bw.got.bed ../test_data/volvox-sorted.coverage.expected.out; | ||
| if [ "$?" != "0" ]; | ||
| then | ||
| echo "ERROR in "$0": Total file comparisons don't match" | ||
| echo "------" | ||
| rm -f ../test_data/bg2bw.got.bed ../test_data/bg2bw.got.bw ../test_data/volvox-sorted.coverage.expected.out | ||
| exit 1 | ||
| fi | ||
|
|
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| rm -f ../test_data/bg2bw.got.bed ../test_data/bg2bw.got.bw ../test_data/volvox-sorted.coverage.expected.out |
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