update module: PERBASE

[camlloyd]

PR checklist

Closes #9794 by bumping perbase version and using topic channels

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[mashehu]

Any idea why the results changed in the new version?

[camlloyd]

One explanation is the COUNT_OF_MATE_RESOLUTIONS column that was introduced in version 1.1.0.

[camlloyd]

Let's investigate how the output looks.

[camlloyd]

Before:

REF	POS	REF_BASE	DEPTH	A	C	G	T	N	R	Y	S	W	K	M	INS	DEL	REF_SKIP	FAIL	NEAR_MAX_DEPTH
chr21	5011214	T	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False
chr21	5011215	C	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	False
chr21	5011216	A	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
chr21	5011217	A	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
chr21	5011218	T	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
chr21	46664973	T	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	False
chr21	46664974	A	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
chr21	46664975	T	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	False
chr21	46664976	A	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
chr21	46664977	T	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False

1558238 rows × 20 columns

After:

REF	POS	REF_BASE	DEPTH	A	C	G	T	N	R	...	S	W	K	M	INS	DEL	REF_SKIP	FAIL	COUNT_OF_MATE_RESOUTIONS	NEAR_MAX_DEPTH
chr21	5011214	T	1	0	0	0	1	0	0	...	0	0	0	0	0	0	0	0	0	False
chr21	5011215	C	1	0	1	0	0	0	0	...	0	0	0	0	0	0	0	0	0	False
chr21	5011216	A	1	1	0	0	0	0	0	...	0	0	0	0	0	0	0	0	0	False
chr21	5011217	A	1	1	0	0	0	0	0	...	0	0	0	0	0	0	0	0	0	False
chr21	5011218	T	1	0	0	0	1	0	0	...	0	0	0	0	0	0	0	0	0	False
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
chr21	46664973	T	2	0	0	0	2	0	0	...	0	0	0	0	0	0	0	0	0	False
chr21	46664974	A	2	2	0	0	0	0	0	...	0	0	0	0	0	0	0	0	0	False
chr21	46664975	T	2	0	0	0	2	0	0	...	0	0	0	0	0	0	0	0	0	False
chr21	46664976	A	2	2	0	0	0	0	0	...	0	0	0	0	0	0	0	0	0	False
chr21	46664977	T	1	0	0	0	1	0	0	...	0	0	0	0	0	0	0	0	0	False

1558238 rows × 21 columns

[camlloyd]

In fact, there is a typo in the output column COUNT_OF_MATE_RESOUTIONS. This should be fixed in version 1.3.0, but it isn't available on bioconda yet.