rwhetten

Must the `--dump-kbm` command be used to save a file to be loaded with `--load-alignments`, or can the ${prefix}.alignments.gz file produced by the program be used directly? When I use...

I am also having the same issue - @almiheenko, can you help?

I am by no means proficient in python, so please correct me if I misunderstood the code. A search `grep -n "np.int32" gapless.py` returned three lines of code: `217: return...

I used `sed 's/np.int32/np.int64/g' gapless.py > gapless64.py` to change all occurrences of np.int32 in gapless.py to np.int64, and modified gapless.sh to call gapless64.py. I also modified gapless.sh to create and...

I added a new line after line 380 of gapless.py (which starts with `opt_par = minimize(CovChi2, [mean, 1/2]...`) to print the values of the opt_par list, e.g. `print("The opt_par values...

I tried another approach, inserting a print command after line 385 in gapless.py to report values of the linex and liney variables, i.e. `print("The values of linex and liney are",x_values,nbinom.pmf(x_values,opt_par[0],opt_par[1])*100)`....

I added line 381 to gapless.py (64-bit version): `print("The opt_par values are",opt_par,"; mean value is",mean,"; pd.DataFrame values are ",pd.DataFrame({'x':probs.loc[selection, 'count'], 'y':probs.loc[selection, 'nbin_cumsum']/probs.loc[selection, 'nbin_sum']}))` The output was ``` The opt_par values...

My gapless conda env (which just provides the python dependencies, not the gapless.py or gapless.sh code) has scipy 1.9.3 - is the requirement for scipy = 1.7.0, or scipy >=...

I understand the virtues of splitting the giant genome into 10 or more smaller "subgenomes", but I want to be sure I understand how to implement that with Gapless. For...