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Fix wrong coordinate from genomic indels, Fix no ref/alt errors. Add genePred support to allow users to easily load their own transcripts #54

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Fix wrong coordinate from genomic indels, Fix no ref/alt errors. Add genePred support to allow users to easily load their own transcripts #54

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Commits on Mar 16, 2020

  1. Patch on top of latest counsyl/hgvs - indel resolution. Load genePred… 

    … files
    @davmlaw
    davmlaw committed Mar 16, 2020
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  2. Unit tests for previously failing HGVS names

    @davmlaw
    davmlaw committed Mar 16, 2020
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Commits on Apr 22, 2020

  1. Populate alt for values like NC_000001.11:g.169549811=

    @davmlaw
    davmlaw committed Apr 22, 2020
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Commits on Apr 29, 2020

  1. Support mito (ie "m.")

    @davmlaw
    davmlaw committed Apr 29, 2020
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  2. Revert "Support mito (ie "m.")" 

    This reverts commit 00a2205.
    @davmlaw
    davmlaw committed Apr 29, 2020
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Commits on May 12, 2021

  1. Support n. (non-coding) ie counsyl#7

    @davmlaw
    davmlaw committed May 12, 2021
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Commits on Sep 7, 2021

  1. Make sure non-coding doesn't have 5' or 3' UTR offsets

    @davmlaw
    davmlaw committed Sep 7, 2021
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Commits on Oct 12, 2021

  1. Refactor - move functions into methods

    @davmlaw
    davmlaw committed Oct 12, 2021
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  2. Start of cDNA matching code changes. Put everything through 1 path as… 

    … exons are just a special case of alignments with no gaps
    @davmlaw
    davmlaw committed Oct 12, 2021
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Commits on Oct 13, 2021

  1. Handle gaps

    @davmlaw
    davmlaw committed Oct 13, 2021
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  2. Handle gaps - put back exons as we need them to work out flanking

    @davmlaw
    davmlaw committed Oct 13, 2021
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Commits on Oct 14, 2021

  1. checkpoint - handle flanking

    @davmlaw
    davmlaw committed Oct 14, 2021
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  2. Finish off gap handling code

    @davmlaw
    davmlaw committed Oct 14, 2021
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  3. linting

    @davmlaw
    davmlaw committed Oct 14, 2021
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Commits on Oct 15, 2021

  1. Keep module interface the same

    @davmlaw
    davmlaw committed Oct 15, 2021
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  2. Better errors, note about not using single=True

    @davmlaw
    davmlaw committed Oct 15, 2021
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  3. Keep module interface the same

    @davmlaw
    davmlaw committed Oct 15, 2021
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  4. Don't die in gaps when going the other way. Change testing data

    @davmlaw
    davmlaw committed Oct 15, 2021
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  5. Always use cDNA as exons, to handle those strange cases like eg NM_00… 

    …1135649.3
    @davmlaw
    davmlaw committed Oct 15, 2021
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Commits on Oct 18, 2021

  1. Make sure to include models in package

    @davmlaw
    davmlaw committed Oct 18, 2021
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Commits on Oct 22, 2021

  1. Better error message

    @davmlaw
    davmlaw committed Oct 22, 2021
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  2. Data generation scripts

    @davmlaw
    davmlaw committed Oct 22, 2021
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Commits on Oct 27, 2021

  1. Keep track of what other contigs we have coordinates for (eg chrX and… 

    … chrY)
    @davmlaw
    davmlaw committed Oct 27, 2021
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Commits on Oct 28, 2021

  1. For non-coding, PyHGVS has cds_start = end not start (so coding lengt… 

    …h = 0)
    @davmlaw
    davmlaw committed Oct 28, 2021
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Commits on Nov 10, 2021

  1. Use transcript offsets rather than exon lengths so we handle gaps pro… 

    …perly
    @davmlaw
    davmlaw committed Nov 10, 2021
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  2. Simplify and make consistent

    @davmlaw
    davmlaw committed Nov 10, 2021
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  3. Previous change didn't work on negative strand

    @davmlaw
    davmlaw committed Nov 10, 2021
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  4. Make sure exons are sorted correctly

    @davmlaw
    davmlaw committed Nov 10, 2021
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Commits on Nov 15, 2021

  1. Support LRG transcripts (was setting as gene not transcripts if no ge… 

    …ne provided)
    @davmlaw
    davmlaw committed Nov 15, 2021
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Commits on Nov 16, 2021

  1. Use ref for alt on any reference HGVS

    @davmlaw
    davmlaw committed Nov 16, 2021
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  2. Validate coordinate span and reference are the same, as eg c.1727_174… 

    …0dup14 should pass but c.1727_1740dup9999 should fail
    @davmlaw
    davmlaw committed Nov 16, 2021
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  3. Support mitochondria

    @davmlaw
    davmlaw committed Nov 16, 2021
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Commits on Nov 24, 2021

  1. Bump version so I can track it

    @davmlaw
    davmlaw committed Nov 24, 2021
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Commits on Dec 9, 2021

  1. HGVS issue counsyl#61 - Reference HGVS without reference base leads t… 

    …o wrong coordinates and reference allele as it treats last digit as ref digit multiplying N that many times
    @davmlaw
    davmlaw committed Dec 9, 2021
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  2. Bump version, add changelog

    @davmlaw
    davmlaw committed Dec 9, 2021
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Commits on Jan 14, 2022

  1. Use same code for calculating transcript position of start/stop codon… 

    …s. Be able to pass in pre-calculated values to save calculation if available
    @davmlaw
    davmlaw committed Jan 14, 2022
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  2. Changelog

    @davmlaw
    davmlaw committed Jan 14, 2022
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  3. No need to sort before storing as we don't rely on order and re-sort … 

    …when loading in utils
    @davmlaw
    davmlaw committed Jan 14, 2022
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  4. Including coding start/end transcript coords if available

    @davmlaw
    davmlaw committed Jan 14, 2022
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Commits on Jan 17, 2022

  1. Fix syntax error

    @davmlaw
    davmlaw committed Jan 17, 2022
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Commits on Aug 1, 2022

  1. Fix issue where dups always matched ref allele

    @davmlaw
    davmlaw committed Aug 1, 2022
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Commits on Aug 18, 2022

  1. Generating transcripts is now handled via https://github.com/SACGF/cdot

    @davmlaw
    davmlaw committed Aug 18, 2022
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Commits on Apr 12, 2023

  1. Support for coord range + equals ie "NC_000010.10:g.89623915_89623920="

    @davmlaw
    davmlaw committed Apr 12, 2023
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  2. Bump version

    @davmlaw
    davmlaw committed Apr 12, 2023
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Commits on May 25, 2023

  1. counsyl#57 - c. dup converted back to delins

    @davmlaw
    davmlaw committed May 25, 2023
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Commits on Jun 1, 2023

  1. bump version

    @davmlaw
    davmlaw authored Jun 1, 2023
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Commits on Jun 14, 2023

  1. Use min of 100 again for normalization window space

    @davmlaw
    davmlaw committed Jun 14, 2023
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