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An option to output SEQ field for secondary alignment (#687)

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* a new option --secondary-seq to output SEQ field for secondary alignments

* comments removed

* Fixed a conflict in #687

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Co-authored-by: Heng Li <lh3@me.com>
This commit is contained in:
Mikhail Kolmogorov
2023-04-21 11:06:13 -04:00
committed by GitHub
co-authored by Heng Li
parent fc24c8a348
commit 704fbc6f5c
3 changed files with 9 additions and 4 deletions
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minimap.h
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@@ -43,6 +43,7 @@
#define MM_F_NO_INV (0x200000000LL)
#define MM_F_NO_HASH_NAME (0x400000000LL)
#define MM_F_SPLICE_OLD (0x800000000LL)
#define MM_F_SECONDARY_SEQ (0x1000000000LL) //output SEQ field for seqondary alignments using hard clipping
#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2