Redo Tao data vignette

[CDieterich]

I think the current meta-condition vignette is outdated.

I would like to prepare for a new vignette

@piechottam - how can we start best from

rmDup_HIVRT_RC13_call2_result.out.gz
rmDup_HIVRT_RC13_rtarrest_plain_result.out.gz
rmDup_SIIIRTMg_RC13_call2_result.out.gz
rmDup_SIIIRTMg_RC13_rtarrest_plain_result.out.gz
rmDup_SIIIRTMn_RC13_call2_result.out.gz
rmDup_SIIIRTMn_RC13_rtarrest_plain_result.out.gz

under
repository/JACUSAnalysis/TestCase/case1

using JACUSA2helper ?

[CDieterich]

Qi did it in repository/JACUSAnalysis/TestCase/test.Rmd.. but without JACUSA2helper, which is a drag.

[CDieterich]

annotation would be repository/JACUSAnalysis/TestCase/case1/rnam.bed (T==C)

I noticed that you used repository/JACUSA2helper/data-raw/DATASET.R
to generate the data set.. This needs to be adapted.

[CDieterich]

In the end, we need a data structure that contains
[5] "HIV.call2.score" "HIV.call2.score.plus1"
[7] "HIV.deletion.score" "HIV.deletion.score.plus1"
[9] "HIV.insertion.score" "HIV.insertion.score.plus1"
[11] "SMg.call2.score" "SMg.call2.score.plus1"
[13] "SMg.deletion.score" "SMg.deletion.score.plus1"
[15] "SMg.insertion.score" "SMg.insertion.score.plus1"
[17] "SMn.call2.score" "SMn.call2.score.plus1"
[19] "SMn.deletion.score" "SMn.deletion.score.plus1"
[21] "SMn.insertion.score" "SMn.insertion.score.plus1"
[23] "HIV.arrest.score" "HIV.arrest.score.plus1"
[25] "SMg.arrest.score" "SMg.arrest.score.plus1"
[27] "SMn.arrest.score" "SMn.arrest.score.plus1"

where plus1 means U/T position + 1