oncoprint - allow adding gaps to string-valued clinical tracks

[adamabeshouse]

closes cBioPortal/cbioportal#3336

[jjgao]

Nice! Could you connect the issue and use closing keywords in the comment.

[jjgao]

For this query, if you sort by Sex and then Show gaps, the gap is not in the right place.

[adamabeshouse]

@jjgao fixed the issue.

It was an interesting bug: I determine the position of each column in the shader, part of this is a binary search which checks the list of gap locations to figure out how many gaps are before a column.

Here's where it gets tricky - the shader language does not allow while loops. So instead I was using a for loop and estimating the number of loops I would need, at maximum, to fully execute the binary search. I made an error there and so the binary search was terminating too early in this case and not computing the right offset.

I fixed it by rewriting the for loop like this for (int i=0; i<1/0; i++) to simulate a while loop (I was surprised that this is allowed).

[Sjoerd-van-Hagen]

@adamabeshouse

I fixed it by rewriting the for loop like this for (int i=0; i<1/0; i++) to simulate a while loop (I was surprised that this is allowed).

In most languages for is just syntactic sugar for while

for ( int i = 0; i < n; i++ )
  //do stuff`

equals

int i = 0
while i < n
  //do stuff
  i++

So any while-true-loop can be written as
for (; true ;)

I am wondering about the i<1/0, is it not easier to just put true or 1<2 to make it more obvious what your intention is? What do you get from the 1/0, I am guessing some infinity value, and not a division by zero error?

[adamabeshouse]

@Sjoerd-van-Hagen the issue is that webgl shader language has very specific rules, including that true and 1<2 are not valid conditions for a for loop. however, i<1/0 is. it can also be done as for(int i=0; i==0; i+=0), but I don't think thats more clear than for(int i=0; i<1/0; i++). yes 1/0 is infinity

[adamabeshouse]

https://deploy-preview-2926--cbioportalfrontend.netlify.com/results?Z_SCORE_THRESHOLD=2.0&cancer_study_id=coadread_tcga_pub&cancer_study_list=coadread_tcga_pub&case_set_id=coadread_tcga_pub_nonhypermut&clinicallist=SEX%2CCANCER_TYPE_DETAILED&gene_list=KRAS%20NRAS%20BRAF&gene_set_choice=user-defined-list&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations