bam file displays error on IGV

[AssumeAssume]

❯ chromap --version
0.1-r208
❯ which igv.sh
~/IGV_Linux_2.8.12/igv.sh

When loading the chromap-mapped（0.1-r208） paried-ended bam file to IGV ( version :Linux 2.8.12 ), the forward reads display fine, but the reverse reads showed lots of mismatches bases. By blatting the reverse reads, I found the mapping position was true but the mistake was due to the direction of the reads, I guess chromap didn't give the true sequence information of the reverse reads in the bam file

[haowenz]

This should be the wrong output sequence in SAM when the reads are mapped on the reverse complementary strand. We will fix this soon. Thank you for testing.

[haowenz]

I pushed a fix for this issue in the latest master branch. It works well on my test dataset. You may test it and see if the issue is resolved. It will be in the next release.