Cannot open BAM files with the SeqAn library
0
0
Entering edit mode
6.1 years ago

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
cpp seqan Bam sequencing • 1.5k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 1868 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6