Question: Cannot open BAM files with the SeqAn library
gravatar for omariqbal2017
10 days 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 • 85 views
ADD COMMENTlink written 10 days ago by omariqbal20170

what is the output of the following command

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


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


ADD REPLYlink modified 10 days ago • written 10 days ago by Pierre Lindenbaum105k

The output of

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


/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"


/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 days ago • written 9 days ago by omariqbal20170

cross posted:

ADD REPLYlink written 6 days ago by Pierre Lindenbaum105k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1586 users visited in the last hour