A. Murat Eren (Meren)

I changed all the things, run the component tests for metagenomics. It may explode later, but it will be easy to fix.

(oh, just remembered: merging this will certainly explode with EcoPhylo when all contigs-db files are generated from scratch -- it will require some attention in #2451)

Florian, based on how you designed the test dataset, is this what you would expect to see for coverage values in anvi'o default:  

Well. I found a way to track primary alignments (it is very ugly and memory intensive), but when I do that, this is what I see from the profiling results...

Just for posterity, this is what does this: ``` diff diff --git a/anvio/bamops.py b/anvio/bamops.py index d70d046ae..39de3ac64 100644 --- a/anvio/bamops.py +++ b/anvio/bamops.py @@ -225,6 +225,13 @@ class BAMFileObject(pysam.AlignmentFile): pysam.AlignmentFile.__init__(self) + #...

We can add a new flag to `anvi-profile` and other relevant programs to `--track-secondary-alignments`, and only then engage all the intensive stuff. But I still don't get why secondary alignments...

Never mind. It needed just a little more work. Here it is with my latest changes:

There is a memory happy way to solve this, and I will do that along with a flag. but now I want to commit these changes and see HOW MUCH...

Because the memory happy way will take even longer than that.

I've been trying to figure that out, but I think it will require me much more time than what I have at the moment. At least COVs / SNVs /...