Anders Pitman

What are some good tools for comparing BAM files to determine if they're semantically the same? ie I need to make sure the data I'm generating matches the output in...

Another question: For the commands listed in the Commands file, what directory did you run each of them from? I'm guessing from within 0_*, 1_*, etc?

Thanks @rachelss. We'll definitely need to have deterministic behavior at each pipeline stage in order to properly do CI. That might not be too difficult. bowtie2 for example appears to...

FYI the [bamUtil diff command](https://genome.sph.umich.edu/wiki/BamUtil:_diff) seems to do exactly what we need for comparing BAM files. I've tested it a bit and even if the files don't match on the...

@rachelss @BobLiterman I'm noticing some strange behavior. When running the command `sisrs alignContigs -p X -a premade -c 0 -f 0_RawData_PremadeGenome -z output` With different values of X for number...

Also noticed 29380 is 2*14690. The other values increase on the same order but are not exact multiples.

@BobLiterman additionally, when running `alignContigs` I haven't been able to get GorGor.bam to match what's in 0_RawData_PremadeGenome, even if I used -p 20 as you did. The output from SISRS...

**Haven't been able to get it to match what's in 1_alignContigs

Strange. Yeah when I run the following command: `~/code/sisrs/SISRS/bin/sisrs alignContigs -p8 -a premade -c 0 -f ~/code/sisrs/SISRS/test_data/0_RawData_PremadeGenome/ -z output1 &> alignContigs_Log1` Snippets from the results are below. You can see...

@BobLiterman I've been trying to get consistent behavior without too much success. I think I've narrowed a good chunk of it down to a specific problem. Can you run the...