| 1 |
#include "GBam.h" |
| 2 |
#include "GArgs.h" |
| 3 |
#include "GStr.h" |
| 4 |
|
| 5 |
#define USAGE "Usage: bamread [--fasta|-a|--fastq|-q|-G|--gff]\n\ |
| 6 |
[-M|--mapped-only|-A|--all] [-o <outfile>] <in.bam>|<in.sam> \n" |
| 7 |
|
| 8 |
|
| 9 |
enum OutType { |
| 10 |
outFASTQ, |
| 11 |
outFASTA, |
| 12 |
outGFF |
| 13 |
}; |
| 14 |
|
| 15 |
OutType out_type=outFASTQ; |
| 16 |
bool all_reads=false; |
| 17 |
bool mapped_only=false; |
| 18 |
|
| 19 |
#define bam_unmapped(b) (((b)->core.flag & BAM_FUNMAP) != 0) |
| 20 |
|
| 21 |
void showfastq(GBamRecord& rec, FILE* fout) { |
| 22 |
if (rec.isMapped() && !all_reads) return; |
| 23 |
if (mapped_only && rec.isUnmapped()) return; |
| 24 |
char* qseq=rec.sequence(); |
| 25 |
fprintf(fout, "@%s\n%s\n", rec.name(), qseq); |
| 26 |
GFREE(qseq); |
| 27 |
qseq=rec.qualities(); |
| 28 |
fprintf(fout, "+\n%s\n",qseq); |
| 29 |
GFREE(qseq); |
| 30 |
} |
| 31 |
|
| 32 |
void showfasta(GBamRecord& rec, FILE* fout) { |
| 33 |
if (rec.isMapped() && !all_reads) return; |
| 34 |
if (mapped_only && rec.isUnmapped()) return; |
| 35 |
char* qseq=rec.sequence(); |
| 36 |
fprintf(fout, ">%s\n%s\n", rec.name(), qseq); |
| 37 |
GFREE(qseq); |
| 38 |
} |
| 39 |
|
| 40 |
void showgff(GBamRecord& rec, FILE* fout) { |
| 41 |
if (rec.isUnmapped()) return; |
| 42 |
char tstrand=rec.spliceStrand(); |
| 43 |
fprintf(fout, "%s\tbam\tmRNA\t%d\t%d\t.\t%c\t.\tID=%s\n", rec.refName(), |
| 44 |
rec.start, rec.end, tstrand, rec.name()); |
| 45 |
for (int i=0;i<rec.exons.Count();i++) { |
| 46 |
fprintf(fout, "%s\tbam\texon\t%d\t%d\t.\t%c\t.\tParent=%s\n", rec.refName(), |
| 47 |
rec.exons[i].start, rec.exons[i].end, tstrand, rec.name()); |
| 48 |
} |
| 49 |
} |
| 50 |
|
| 51 |
int main(int argc, char *argv[]) |
| 52 |
{ |
| 53 |
|
| 54 |
GArgs args(argc, argv, "fasta;fastq;gff;all;help;mapped-only;" |
| 55 |
"hAMGaqo:"); |
| 56 |
args.printError(USAGE, true); |
| 57 |
if (args.getOpt('h') || args.getOpt("help") || args.startNonOpt()==0) { |
| 58 |
GMessage(USAGE); |
| 59 |
return 1; |
| 60 |
} |
| 61 |
args.printCmdLine(stderr); |
| 62 |
|
| 63 |
all_reads=(args.getOpt('A') || args.getOpt("all")); |
| 64 |
mapped_only=(args.getOpt('M') || args.getOpt("mapped-only")); |
| 65 |
if ((all_reads && mapped_only)) { |
| 66 |
GError("Error: incompatible options !\n"); |
| 67 |
} |
| 68 |
|
| 69 |
if (args.getOpt('a') || args.getOpt("fasta")) |
| 70 |
out_type=outFASTA; |
| 71 |
else if (args.getOpt('G') || args.getOpt("gff")) { |
| 72 |
out_type=outGFF; |
| 73 |
mapped_only=true; |
| 74 |
} |
| 75 |
char* fname=args.nextNonOpt(); |
| 76 |
if (fname==NULL || fname[0]==0) { |
| 77 |
GMessage(USAGE); |
| 78 |
return 1; |
| 79 |
} |
| 80 |
GBamReader bamreader(fname); |
| 81 |
FILE* fout=stdout; |
| 82 |
char* outfname=args.getOpt('o'); |
| 83 |
if (outfname) { |
| 84 |
fout=fopen(outfname, "w"); |
| 85 |
if (fout==NULL) { |
| 86 |
fprintf(stderr, "Error creating output file %s\n", outfname); |
| 87 |
return 2; |
| 88 |
} |
| 89 |
} |
| 90 |
GBamRecord *aln=NULL; |
| 91 |
if (out_type==outFASTA) { |
| 92 |
while ((aln=bamreader.next())!=NULL) { |
| 93 |
showfasta(*aln, fout); |
| 94 |
delete aln; |
| 95 |
} |
| 96 |
} |
| 97 |
else if (out_type==outGFF) { |
| 98 |
while ((aln=bamreader.next())!=NULL) { |
| 99 |
showgff(*aln, fout); |
| 100 |
delete aln; |
| 101 |
} |
| 102 |
} |
| 103 |
else { |
| 104 |
while ((aln=bamreader.next())!=NULL) { |
| 105 |
showfastq(*aln, fout); |
| 106 |
delete aln; |
| 107 |
} |
| 108 |
} |
| 109 |
if (fout!=stdout) fclose(fout); |
| 110 |
return 0; |
| 111 |
} |
