shiftGAlignmentsList Error

[samiragarwala]

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]

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 [email protected] 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!

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[samiragarwala]

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 -> <Anonymous> 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]

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