[DOC] Apply review

Signed-off-by: Lydia Buntrock <[email protected]>

doc/tutorial/02_layout/index.md

@@ -48,8 +48,6 @@ raptor layout --input-file all_bin_path.txt --tmax 64
 The `input-file` looks exactly as in our previous calls of `raptor index`; it contains all the paths of our database
 files.
 
-\todo Chopper braucht ein `input_data.tsv` input, wobei es momentan nur eine Spalte (mit den Pfaden) gibt, also geht auch `.txt`.
-
 The parameter `--tmax` limits the number of technical bins on each level of the HIBF. Choosing a good \f$t_{max}\f$ is
 not trivial. The smaller \f$t_{max}\f$, the more levels the layout needs to represent the data. This results in a higher
 space consumption of the index. While querying each individual level is cheap, querying many levels might also lead to
@@ -91,7 +89,7 @@ And use the data of the `1024` Folder.
 \hint
 First we need a file with all paths to the fasta files. For this use the command:
 ```bash
-for i in {0001..1023}; do echo "1024/bins/bin_$i.fasta" >> all_bin_paths.txt; done
+seq -f "1024/bins/bin_%04g.fasta" 0 1 1023 > all_bin_paths.txt
 ```
 \endhint
 
@@ -179,8 +177,6 @@ possible to specify a size here. But we can offer the option to name the desired
 
 \note These parameters must be set identically for `raptor index`.
 
-\todo This is not checked at the moment?
-
 A call could then look like this:
 ```bash
 raptor layout --input-file all_bin_path.txt \
@@ -228,7 +224,8 @@ The first step is to estimate the number of (representative) k-mers per user bin
 [HyperLogLog (HLL) sketches](http://algo.inria.fr/flajolet/Publications/FlFuGaMe07.pdf) of the input data. These HLL
 sketches are stored in a directory and will be used in computing an HIBF layout.
 
-We will also give a short explanation of the HLL sketches here to explain the possible parameters.
+We will also give a short explanation of the HLL sketches here to explain the possible parameters, whereby each bin is
+sketched individually.
 
 \note
 Most parameters are advanced and only need to be changed if the calculation takes significantly too long or the memory
@@ -255,9 +252,6 @@ If we choose our `b` (`m`) to be very large, then we need more memory but get hi
 growing exponentially.) In addition, calculating the layout can take longer with a high `b` (`m`). If we have many user
 bins and observe a long runtime, then it is worth choosing a somewhat smaller `b` (`m`).
 
-\todo
-Wird bisher ein sketch über alles berechnet oder einzelne sketches die gemerged werden? Laut Felix ist das mergen ebenfalls sehr schnell. (zb 10 genome sketchen und dann mergen)
-
 #### Advanced options for HLL sketches
 
 The following options should only be touched if the calculation takes a long time.
@@ -266,21 +260,11 @@ We have implemented another preprocessing that summarises the technical bins eve
 of the input data. This can be switched off with the flag `--skip-similarity-preprocessing` if it costs too much
 runtime.
 
-\todo
-Add parameter `--skip-similarity-preprocessing` instead of `--estimate-union` and `--rearrange-user-bins`. Set it as
-advanced.
-
-\todo
-`--disable-sketch-output` wahrscheinlich unsinnig, da nur der zwischenstand zwischen count und layout
-
 With `--max-rearrangement-ratio` you can further influence a part of the preprocessing (value between `0` and `1`). If
 you set this value to `1`, it is switched off. If you set it to a very small value, you will also need more runtime and
 memory. If it is close to `1`, however, just little re-arranging is done, which could be bad. In our benchmarks, however,
 we were not able to determine a too great influence, so we recommend that this value only be used for fine tuning.
 
-\todo
-Wenn r=1, dann `--rearrange-user-bins` aus, daher die flag nicht nötig.
-
 One last observation about these advanced options: If you expect hardly any similarity in the data set, then the
 similarity preprocessing makes very little difference.
 

doc/tutorial/03_index/index.md

@@ -263,9 +263,6 @@ raptor build --hibf binning.layout \
              --output hibf.index
 ```
 
-\note wichtig!!! --false-positive-rate "$fpr"  muss die selbe sein wie die von raptor Genauso die k-mer size. Hash functions auch oder?
-\warning test
-
 \assignment{Assignment 4: A default HIBF}
 Since we cannot see the advantages of the hibf with our small example. And certainly not the differences when we change
 the parameters. Let's not go back to our small example from above, but to the one from the introduction: