Fix counting reads when sex chromosomes aren't available #26
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NULL doesn't have a dimension, while NA is a vector of length 1 If this is not done, building a PoN with data missing sex chromosomes will fail, because the code will try to bind NA (with dimensions) with NULL (no dimension), leading to a hard-to-debug-message
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Submitted upstream as PR (GavinHaLab/ichorCNA#26 these patches fix breakage seen in real-world usage (DIncalciLab/samurai/commit/5e292cef413676448f503f97660c395ee9ba0d99) However,u pstream development is very slow, and a long time may pass before the PR is accepted
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Submitted upstream as PR (GavinHaLab/ichorCNA#26 these patches fix breakage seen in real-world usage (DIncalciLab/samurai/commit/5e292cef413676448f503f97660c395ee9ba0d99) However,u pstream development is very slow, and a long time may pass before the PR is accepted
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) Submitted upstream as PR (GavinHaLab/ichorCNA#26 these patches fix breakage seen in real-world usage (DIncalciLab/samurai/commit/5e292cef413676448f503f97660c395ee9ba0d99) However,u pstream development is very slow, and a long time may pass before the PR is accepted
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At the moment, creating a PoN without data on chromosome X is bound to fail due to a bug in ichorCNA(GavinHaLab/ichorCNA#26). It is unclear when a new version will be out, so I have patched the current bioconda package (bioconda/bioconda-recipes#61045) and built new container images, which I want to update to in this PR.
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…9531) * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run At the moment, creating a PoN without data on chromosome X is bound to fail due to a bug in ichorCNA(GavinHaLab/ichorCNA#26). It is unclear when a new version will be out, so I have patched the current bioconda package (bioconda/bioconda-recipes#61045) and built new container images, which I want to update to in this PR. * Update some md5sums * Update test snapshot * Update test snapshot
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…9531) * Bump ichorCNA package build in ichorcna/createpon and ichorcna/run At the moment, creating a PoN without data on chromosome X is bound to fail due to a bug in ichorCNA(GavinHaLab/ichorCNA#26). It is unclear when a new version will be out, so I have patched the current bioconda package (bioconda/bioconda-recipes#61045) and built new container images, which I want to update to in this PR. * Update some md5sums * Update test snapshot * Update test snapshot
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If a detected gender is unknown, the median X counts are set to
NULL, and Y counts toNA. However,NULLdoesn't have a dimension, whileNAis a vector of length 1. This will go undetected when doing regular runs, but it will break when creating a new PoN with data without sex chromosomes, because the code will try to bindNA(with dimensions) withNULL(no dimension), leading to a hard-to-debug-message (arguments imply differing number of rows).This is fixed by setting the median chrX value to
NA, and adjusting checks inoutput.Rso that they understand that the value can also beNA(incidentally, the checks for chromosome Y were incomplete, they only checked forNULL, soNAis also taken into account`).This is not a new issue, I believe it has gone unnoticed for years.