blasr bam output problem

[daniellezhang]

I tried to do alignment using blasr. Blasr seems to run fine and gave no error message yet the output bam file is unreable like this:

unix306 631 % blasr ~/data/lambda_phage/lp1d.fasta  ~/data/lambda_phage/lambda_phage_ref.fasta --bam --out aligned.bam
[INFO] 2018-09-24T12:12:18 [blasr] started.
[INFO] 2018-09-24T12:12:19 [blasr] ended.
unix306 632 % cat aligned.bam
?BC\?QKn?@
          ?ˉz?\ ????FBBH?U?    A~]?n?HOSR?U??�??g[~???|?H???]?(Z?8x
V?:s?b???Q?`?W??&?
                  ?vG?)?)??=O?Jg?NaJ]׉ʁ44P???<???@?
                                                   4z@??Bka/Wȉ?Ƶ??K?ΣؾĆ#
??j??'?O??l?tƲjEsE???E??!,k#?y??]??1???R???ie(???4?ߎPe8??@.??        ??GȄ\?I?S?P??]Ǯ72ï? 
?}k'??K?'?@???BCnix306 633 % Sߍ?ȳJ$?R

[mhsieh]

In order "cat" the content of a bam file, I believe you need to use samtools view aligned.bam command