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Indel alignment fix #182

Merged
merged 14 commits into from
Jan 11, 2022
Merged

Indel alignment fix #182

merged 14 commits into from
Jan 11, 2022

Commits on Jan 11, 2022

  1. 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.
    @Colelyman
    Colelyman committed Jan 11, 2022
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  2. 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.
    @Colelyman
    Colelyman committed Jan 11, 2022
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  3. 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.
    @Colelyman
    Colelyman committed Jan 11, 2022
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  4. 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.
    @Colelyman
    Colelyman committed Jan 11, 2022
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  5. 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.
    @Colelyman @kclem
    Colelyman authored and kclem committed Jan 11, 2022
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  6. 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.
    @Colelyman @kclem
    Colelyman authored and kclem committed Jan 11, 2022
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    4db066f View commit details
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  7. 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.
    @Colelyman @kclem
    Colelyman authored and kclem committed Jan 11, 2022
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  8. 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.
    @Colelyman @kclem
    Colelyman authored and kclem committed Jan 11, 2022
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  9. 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.
    @Colelyman @kclem
    Colelyman authored and kclem committed Jan 11, 2022
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  10. 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.
    @Colelyman
    Colelyman committed Jan 11, 2022
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  11. Merge branch 'indel-alignment-fix' of https://github.com/edilytics/CR… 

    …ISPResso2 into indel-alignment-fix
    @kclem
    kclem committed Jan 11, 2022
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  12. 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.
    @kclem
    kclem committed Jan 11, 2022
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  13. 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.
    @Colelyman @kclem
    Colelyman authored and kclem committed Jan 11, 2022
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    55aa4d2 View commit details
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  14. Merge branch 'indel-alignment-fix' of https://github.com/edilytics/CR… 

    …ISPResso2 into indel-alignment-fix
    @kclem
    kclem committed Jan 11, 2022
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