Add an MN:i tag (number of SEQ bases at time of modification tag update). #714
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SAMtags.tex
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| \item[MZ:i:\tagvalue{length}] | ||
| \hfill\\ | ||
| Tools may edit the {\sf SEQ} sequence data, such as modifying the alignment with hard-clipping. | ||
| If the sequence is shrunk in this manner then the base offsets in {\tt MM} and {\tt MM} become invalid unless they are also updated accordingly. |
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| If the sequence is shrunk in this manner then the base offsets in {\tt MM} and {\tt MM} become invalid unless they are also updated accordingly. | |
| If the sequence is shrunk in this manner then the base offsets in {\tt MM} and {\tt ML} become invalid unless they are also updated accordingly. |
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Thanks. Fixed this now
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What does the Z stand for? In #646 (comment), the MZ tag name was just a placeholder: “Add a new tag e.g. |
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Agreed, it's still obviously up for anyone to propose something better. Starting with M is reasonable as it's then with the others. MN may be better as it's then ML, MM, MN in a clump together for the sorted list of tags? N for Number of bases? Z was tentatively just siZe in my head I guess. |
This is used as a sanity check on the validity of the MM and ML tags. It holds the length of SEQ at the time MM and ML were produced and/or updated. The intention is to provide a mechanism to detect hard-clipping has been performed with a tool that is not MM/ML aware. Fixes samtools#646
jkbonfield
changed the title
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As agreed during the last conference call, I renamed MZ to MN. (Mnenomic could be Modification Number of bases?) |
This is used as a sanity check on the validity of the MM and ML tags. It holds the length of SEQ at the time MM and ML were produced and/or updated. The intention is to provide a mechanism to detect hard-clipping has been performed with a tool that is not MM/ML aware.
Fixes #646