shiftGAlignmentsList Error

[Samir Agarwala]

When I try to offset the read starting position using shiftGAlignmentsList, I get the following error:

all(elementNROWS(gal) < 3) is not TRUE
Calls: shiftGAlignmentsList -> stopifnot
Execution halted

It might be relevant that I aligned paired end reads using bwa and then sorted the file to get the BAM file.

I'm not sure what I should change in the BAM processing to get algorithm working and would appreciate any help.

Thank you!

[JIANHONG OU]

If you sort the file correctly, this should not be a problem. Could you share me the bamfile to repeat your error?

…

On Sun, May 5, 2019 at 8:40 PM Samir Agarwala ***@***.***> wrote: When I try to offset the read starting position using shiftGAlignmentsList, I get the following error: all(elementNROWS(gal) < 3) is not TRUE Calls: shiftGAlignmentsList -> stopifnot Execution halted It might be relevant that I aligned paired end reads using bwa and then sorted the file to get the BAM file. I'm not sure what I should change in the BAM processing to get algorithm working and would appreciate any help. Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#15>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABLBEA54W37IND66WMSOGQ3PT55AVANCNFSM4HK4RA4Q> .

-- Yours sincerely, Jianhong Ou

[Samir Agarwala]

I realigned the files to get new BAM files and this problem seems to be resolved. However, when I export the offset reads as a BAM file using export(gal1, shiftedBamfile), I now get the following error:

Error in value[3L] :
'asBam' internal: samtools invoked 'abort'; see warnings() and restart R
SAM file: 'offset_output/shifted.sam'
Calls: export ... tryCatch -> tryCatchList -> tryCatchOne ->
In addition: Warning messages:
1: In .local(object, con, format, ...) :
these classes are not yet valid for BAM tag export: logical, logical, logical
2: In mapply(FUN = FUN, ..., SIMPLIFY = SIMPLIFY) :
longer argument not a multiple of length of shorter
3: In mapply(FUN = FUN, ..., SIMPLIFY = SIMPLIFY) :
longer argument not a multiple of length of shorter
4: In doTryCatch(return(expr), name, parentenv, handler) :
Parse error at line 94: missing colon in auxiliary data
Execution halted

[JIANHONG OU]

I am trying to fix the bug. Please have a try with the newest development version.