Indel alignment fix (#182)

* 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.

* 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.

* 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.

* 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.

* 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.

* 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.

* 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.

* 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.

* 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.

* 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.

* Squashed commit of the following:

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.

* 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.

Co-authored-by: Kendell Clement <k.clement.dev@gmail.com>