commit 8564eb0
Merge: f6ef62c 07cc7d8
Author: Kendell Clement <k.clement.dev@gmail.com>
Date:   Tue Jan 11 16:20:15 2022 -0500

    Merge branch 'indel-alignment-fix' of https://github.com/edilytics/CRISPResso2 into indel-alignment-fix

commit 07cc7d8
Author: Cole Lyman <cole@colelyman.com>
Date:   Fri Dec 10 15:29:59 2021 -0700

    Fix bug in `find_indels_substitutions`

    This bug occurred when there was a deletion at the end of a sequence, and was
    thus not properly accounted for.

commit f6ef62c
Author: Cole Lyman <cole@colelyman.com>
Date:   Fri Dec 10 15:29:59 2021 -0700

    Fix bug in `find_indels_substitutions`

    This bug occurred when there was a deletion at the end of a sequence, and was
    thus not properly accounted for.

commit 7212f87
Author: Cole Lyman <cole@colelyman.com>
Date:   Fri Dec 10 15:26:17 2021 -0700

    Add a unit test for `find_indels_substitutions`

    This unit test checks for deletions at the end of a sequence, which are
    inherently outside of the include_indx_set window.

commit d50b4e9
Author: Cole Lyman <cole@colelyman.com>
Date:   Fri Dec 10 15:03:22 2021 -0700

    Fix a bug in `find_indels_substitutions`

    The bug that this commit fixes is when an insertion occurs at the edge of the
    include indexes. The trouble with this earlier was that it was using the `idx`
    to calculate the size of the insertion, but the `idx` wasn't being incremented
    anymore because it was outside of the include window.

commit 4db066f
Author: Cole Lyman <cole@colelyman.com>
Date:   Fri Dec 10 15:01:39 2021 -0700

    Add test case for `find_indels_substitutions`

    This test case is extracted from the CRISPRessoBatch integration test and
    provides an example where there is an insertion at the edge of the include
    index.

commit 3b3a741
Author: Cole Lyman <cole@colelyman.com>
Date:   Fri Dec 10 11:37:07 2021 -0700

    Fix bug in CRISPRessoCompare where sample names were not properly set

    This was a place where it was (partially) missed during the crispresso2_info
    object refactoring.

commit e9f5eff
Author: Cole Lyman <cole@colelyman.com>
Date:   Fri Dec 10 15:26:17 2021 -0700

    Add a unit test for `find_indels_substitutions`

    This unit test checks for deletions at the end of a sequence, which are
    inherently outside of the include_indx_set window.

commit d4d45a9
Author: Cole Lyman <cole@colelyman.com>
Date:   Fri Dec 10 15:03:22 2021 -0700

    Fix a bug in `find_indels_substitutions`

    The bug that this commit fixes is when an insertion occurs at the edge of the
    include indexes. The trouble with this earlier was that it was using the `idx`
    to calculate the size of the insertion, but the `idx` wasn't being incremented
    anymore because it was outside of the include window.

commit 13f00bb
Author: Cole Lyman <cole@colelyman.com>
Date:   Fri Dec 10 15:01:39 2021 -0700

    Add test case for `find_indels_substitutions`

    This test case is extracted from the CRISPRessoBatch integration test and
    provides an example where there is an insertion at the edge of the include
    index.

commit 659ae34
Author: Cole Lyman <cole@colelyman.com>
Date:   Fri Dec 10 11:37:07 2021 -0700

    Fix bug in CRISPRessoCompare where sample names were not properly set

    This was a place where it was (partially) missed during the crispresso2_info
    object refactoring.

If many runs are run at the same time, batch summary plots may fail because they are too large for matplotlib. This parameter `--suppress_batch_summary_plots` allows individual runs to be plotted, but suppresses batch summary plots that may otherwise be too big.

Remove max sample limit for plotting

Parameterize the max number of samples to plot on each page of reports. Additional PDFs will be created with this number of samples on them.

…fication types

These heatmaps are interactive (zoomable and panable) and show for each sample
the percentage of insertions, substitutions, and deletions.

This is mainly so that we can use the fullscreen modal functionality in this version.

I have tried countless different ways for this to work, and this is the best
that I can come up with. After the modal is opened it triggers the plot to
resize, and then for some reason you need to trigger the resize event. I think
this is because a `div` changing size won't actually trigger the resizing of the
plot (and neither will just calling `Plotly.Plots.resize`...?!).

I'm pretty sure the autosize doesn't do anything, but it is there for good
measure.

This includes removing the Bootstrap modal (two out of the three plots would
resize properly and I couldn't figure out a way to have the plot displayed
outside of the modal). I have left in some javascript to make the plot
fullscreen, but I couldn't get the formatting quite right and the plot wasn't
much bigger in the fullscreen version because there was a ton of space between
the plot and the heatmap. If some brave soul would like to tackle it, feel free!

I have consolidated how the plot data is passed around, so that now you can pass
in only one dict with all of the information instead of 4 or 5 separate
parameters. I also renamed the `heatmap_plot_*` to
`allele_modification_heatmap_*`.

This also includes correctly resizing the plot when the line plot tab is
selected!

The plot that is suppressed is the large nucleotide quilt when there is a large
number of samples. Is it okay to suppress this plot @kclem?

…ples

If many runs are run at the same time, batch summary plots may fail because they are too large for matplotlib. This parameter `--suppress_batch_summary_plots` allows individual runs to be plotted, but suppresses batch summary plots that may otherwise be too big.

Remove max sample limit for plotting

Parameterize the max number of samples to plot on each page of reports. Additional PDFs will be created with this number of samples on them.

…fication types

These heatmaps are interactive (zoomable and panable) and show for each sample
the percentage of insertions, substitutions, and deletions.

This is mainly so that we can use the fullscreen modal functionality in this version.

I have tried countless different ways for this to work, and this is the best
that I can come up with. After the modal is opened it triggers the plot to
resize, and then for some reason you need to trigger the resize event. I think
this is because a `div` changing size won't actually trigger the resizing of the
plot (and neither will just calling `Plotly.Plots.resize`...?!).

I'm pretty sure the autosize doesn't do anything, but it is there for good
measure.

This includes removing the Bootstrap modal (two out of the three plots would
resize properly and I couldn't figure out a way to have the plot displayed
outside of the modal). I have left in some javascript to make the plot
fullscreen, but I couldn't get the formatting quite right and the plot wasn't
much bigger in the fullscreen version because there was a ton of space between
the plot and the heatmap. If some brave soul would like to tackle it, feel free!

I have consolidated how the plot data is passed around, so that now you can pass
in only one dict with all of the information instead of 4 or 5 separate
parameters. I also renamed the `heatmap_plot_*` to
`allele_modification_heatmap_*`.

This also includes correctly resizing the plot when the line plot tab is
selected!

The plot that is suppressed is the large nucleotide quilt when there is a large
number of samples. Is it okay to suppress this plot @kclem?

…ples

…Resso2 into largeAggregation

When not running CRISPRessoAggregate, default values for the
`allele_modification_heatmap_plot` and `allele_modification_lin_plot`
dictionaries will be set so that the template can be properly rendered.

… handled

…ellolab#212)

* Batch type coerce and r2 file check

* Revert "Batch type coerce and r2 file check"

This reverts commit f917366.

* Coerce int values

If multiple qwcs were provided in batch mode, a parsing error would occur. This fixes this bug.

Evidently old pandas versions throw an error if a column doesn't exist. This checks to see if the column exists before the values are set.

Also, only open and shutdown the process pool when necessary.