BWA 0.5.9rc1

[juan]

Being the early adopter, I tried using the -r option in bwa sampe from the latest version of bwa. If I understand correctly, this option will add the specified @RG tag to the SAM output file.
Has anyone else tried this? How does it work? I tried adding the following option and get an error

bwa sampe -P -a 1000 -r '@RG\tID:what\tCN:where\tDS:why\tDT:when\tPL:ILLUMINA\tPU:how\tSM:who' -f f1.sam human_g1k_v37.fasta f1_1.sai f1_2.sai f1.fq f2.fq

The error I get is
[bam_header_read] invalid BAM binary header (this is not a BAM file).

[Mali Salmon]

Got the same error (using the same version), even without using -r

[jyli]

Being the early adopter, I tried using the -r option in bwa sampe from the latest version of bwa. If I understand correctly, this option will add the specified @RG tag to the SAM output file.
Has anyone else tried this? How does it work? I tried adding the following option and get an error

bwa sampe -P -a 1000 -r '@RG\tID:what\tCN:where\tDS:why\tDT:when\tPL:ILLUMINA\tPU:how\tSM:who' -f f1.sam human_g1k_v37.fasta f1_1.sai f1_2.sai f1.fq f2.fq

The error I get is
[bam_header_read] invalid BAM binary header (this is not a BAM file).

Hi, there

I tried similar thing, but it gave me different errors:

bwa sampe -P -a 334 -r '@RG\tID:dodrp445981_1_2_13052011\tSM:dodrp445981\tLB:ga\tPL:Illumina'

Error:

malformated @RG line

Can anyone help here??

[jyli]

Being the early adopter, I tried using the -r option in bwa sampe from the latest version of bwa. If I understand correctly, this option will add the specified @RG tag to the SAM output file.
Has anyone else tried this? How does it work? I tried adding the following option and get an error

bwa sampe -P -a 1000 -r '@RG\tID:what\tCN:where\tDS:why\tDT:when\tPL:ILLUMINA\tPU:how\tSM:who' -f f1.sam human_g1k_v37.fasta f1_1.sai f1_2.sai f1.fq f2.fq

The error I get is
[bam_header_read] invalid BAM binary header (this is not a BAM file).

Hi, there

I tried similar thing, but it gave me different errors:

bwa sampe -P -a 334 -r '@RG\tID:dodrp445981_1_2_13052011\tSM:dodrp445981\tLB:ga\tPL:Illumina'

Error:

malformated @RG line

Can anyone help here??

Actually, I found the piece of C code in bwa, BUT, I never programmed in "C"

while ((c = getopt(argc, argv, "a:sPn:N:c:f:Ar:")) >= 0) {
switch (c) {
case 'r':
if (bwa_set_rg(optarg) < 0) {
fprintf(stderr, "[%s] malformated @RG line\n", __func__);
return 1;
}
break;