Add rd depth tag from hifiasm #171
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rd=n means that n+1 reads were used to construct the node.
milenovic
changed the title
graph/assemblygraphbuilder.cpp
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| @@ -422,6 +423,9 @@ namespace io { | |||
| } else if (auto kaTag = gfa::getTag<float>("ka", record.tags)) { | |||
| graph.m_depthTag = "ka"; | |||
| nodeDepth = *kaTag; | |||
| } else if (auto rdTag = gfa::getTag<int64_t>("rd", record.tags)) { | |||
| graph.m_depthTag = "rd"; | |||
| nodeDepth = *rdTag; | |||
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I am not sure this is a correct approach. Let's say you had 10 reads, then it will be shown as 10x depth here. In the same time for a longer node containing 1000 reads it will be shown as 1000x which is not quite correct.
This will confuse e.g. coloring using node depths, etc. I think you'd need to handle rd pretty much similar to a standard GFA RC tag (which is read count). This way we will have proper read depth value.
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Aplogies, I did misunderstand the tag. Just got a reply from hifiasm developer.
Which says that rd:i:n is indeed coverage, not the number of reads.
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So, if this is really a coverage depth, why it is an integer value?
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It just rounds down a integer number.
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Ah, ok. Thanks for the clarification!
hifiasm shows coverage as in rd:i:n tag where coverage is n+1.
graph/assemblygraphbuilder.cpp
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| @@ -422,6 +423,9 @@ namespace io { | |||
| } else if (auto kaTag = gfa::getTag<float>("ka", record.tags)) { | |||
| graph.m_depthTag = "ka"; | |||
| nodeDepth = *kaTag; | |||
| } else if (auto rdTag = gfa::getTag<int64_t>("rd", record.tags)) { | |||
| graph.m_depthTag = "rd"; | |||
| nodeDepth = *rdTag; | |||
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Ah, ok. Thanks for the clarification!
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I just made another change to add/subtract 1 when reading/saving GFA, as showing depth of 0x would be very confusing to the user. |
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Linux fails are unrelated – looks like due to changes in GitHub Linux runner images |
rd:i:n means that n+1 reads were used to construct the node. I decided to show the raw rd value instead of adding 1 to it.