[FIX] Add duplicated sequences to output and fix vcf output #208
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## master #208 +/- ##
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- Coverage 98.35% 98.34% -0.01%
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Lines 850 848 -2
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To discuss: What is the length of a tandem duplication.
I had a quick look at the specification (source) and I found that
SVLEN = Difference in length between REF and ALT alleles
Therefore, I would change the length to 27 in your example.
However, it feels a bit redundant to me that SVLEN is always END-POS, because it doesn't add information.
| // The SVLEN is neither too short nor too long than specified by the user. | ||
| if (std::abs(sv_length) >= args.min_var_length && | ||
| std::abs(sv_length) <= args.max_var_length) | ||
| std::abs(sv_length) <= args.max_var_length && | ||
| ((sv_type != "DUP" || sv_type != "INS") || insert_size <= args.max_tol_deleted_length) && |
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I don't understand this condition, and (sv_type != "DUP" || sv_type != "INS") is always true.
Also note that our definition of SVLEN has impact here.
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Ah damn my summary has ruined it 😅 thx for the hint
| if (mate1.orientation == strand::forward) | ||
| { | ||
| size_t insert_size = cluster.get_average_inserted_sequence_size(); |
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| size_t insert_size = cluster.get_average_inserted_sequence_size(); | |
| size_t const insert_size = cluster.get_average_inserted_sequence_size(); |
The three if-statements above can be merged into a single one.
Yes, but the SVLEN is not used everywhere, I found a discussion about INVs here. Maybe we just introduce a second INFO value beside the SVLEN. I will adjust the PR. |
Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>
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| if (mate1.orientation == mate2.orientation) | ||
| { | ||
| if (mate1.seq_name == mate2.seq_name) | ||
| { | ||
| size_t insert_size = cluster.get_average_inserted_sequence_size(); | ||
| if (mate1.orientation == strand::forward) | ||
| { |
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These could be merged into one condition
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You mean the two if cases?
I opened this PR because I actually want to call INVs. For calling INVs there will be an else for if (mate1.orientation == mate2.orientation). So I would leave this as it is.
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The three nested if cases actually...
Of course, if you add else branches later, then it won't be possible.
| } | ||
| } | ||
| } |
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because they end in the same place.
This PR adds the duplicated sequence to the output.
To discuss: What is the length of a tandem duplication. In this PR I decided to use the length of the duplicated sequence.
For example:
Than the duplication goes from (5, 23],
its duplicated sequence is AAACCCGGG
and the SVLEN is 9.