Question: Cannot open BAM files with the SeqAn library
0
gravatar for omariqbal2017
9 months ago by
omariqbal20170 wrote:

For some reason, I cannot open BAM files using the SeqAn library. While I try to open by executing the following code:

CharString bamFileName = getAbsolutePath("demos/tutorial/sam_and_bam_io/example.bam");

I get the following error:

ERROR: Could not open /home/omair/Programs/seqan/demos/tutorial/sam_and_bam_io/example.bam

c++ seqan bam sequencing • 328 views
ADD COMMENTlink written 9 months ago by omariqbal20170

what is the output of the following command

file /home/omair/Programs/seqan/demos/tutorial/sam_and_bam_io/example.bam

and

find  /home/omair/ -type f -name "example.bam"

?

ADD REPLYlink modified 9 months ago • written 9 months ago by Pierre Lindenbaum115k

The output of

file /home/omair/Programs/seqan/demos/tutorial/sam_and_bam_io/example.bam

is

/home/omair/Programs/seqan/demos/tutorial/sam_and_bam_io/example.bam: gzip compressed data, extra field

and the output of

find /home/omair/ -type f -name "example.bam"

is

/home/omair/Programs/seqan/apps/ngs_roi/example/example.bam /home/omair/Programs/seqan/demos/tutorial/file_io_overview/example.bam /home/omair/Programs/seqan/demos/tutorial/sam_and_bam_io/example.bam

ADD REPLYlink modified 9 months ago • written 9 months ago by omariqbal20170

cross posted: https://bioinformatics.stackexchange.com/questions/3871

ADD REPLYlink written 9 months ago by Pierre Lindenbaum115k
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