mm_mapopt_t

minimap2_sys

Struct mm_mapopt_t 

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#[repr(C)]
pub struct mm_mapopt_t {
Show 60 fields
    pub flag: i64,
    pub seed: c_int,
    pub sdust_thres: c_int,
    pub max_qlen: c_int,
    pub bw: c_int,
    pub bw_long: c_int,
    pub max_gap: c_int,
    pub max_gap_ref: c_int,
    pub max_frag_len: c_int,
    pub max_chain_skip: c_int,
    pub max_chain_iter: c_int,
    pub min_cnt: c_int,
    pub min_chain_score: c_int,
    pub chain_gap_scale: f32,
    pub chain_skip_scale: f32,
    pub rmq_size_cap: c_int,
    pub rmq_inner_dist: c_int,
    pub rmq_rescue_size: c_int,
    pub rmq_rescue_ratio: f32,
    pub mask_level: f32,
    pub mask_len: c_int,
    pub pri_ratio: f32,
    pub best_n: c_int,
    pub alt_drop: f32,
    pub a: c_int,
    pub b: c_int,
    pub q: c_int,
    pub e: c_int,
    pub q2: c_int,
    pub e2: c_int,
    pub transition: c_int,
    pub sc_ambi: c_int,
    pub noncan: c_int,
    pub junc_bonus: c_int,
    pub junc_pen: c_int,
    pub zdrop: c_int,
    pub zdrop_inv: c_int,
    pub end_bonus: c_int,
    pub min_dp_max: c_int,
    pub min_ksw_len: c_int,
    pub anchor_ext_len: c_int,
    pub anchor_ext_shift: c_int,
    pub max_clip_ratio: f32,
    pub rank_min_len: c_int,
    pub rank_frac: f32,
    pub pe_ori: c_int,
    pub pe_bonus: c_int,
    pub jump_min_match: i32,
    pub mid_occ_frac: f32,
    pub q_occ_frac: f32,
    pub min_mid_occ: i32,
    pub max_mid_occ: i32,
    pub mid_occ: i32,
    pub max_occ: i32,
    pub max_max_occ: i32,
    pub occ_dist: i32,
    pub mini_batch_size: i64,
    pub max_sw_mat: i64,
    pub cap_kalloc: i64,
    pub split_prefix: *const c_char,

}

Fields§

§flag: i64§seed: c_int§sdust_thres: c_int§max_qlen: c_int§bw: c_int§bw_long: c_int§max_gap: c_int§max_gap_ref: c_int§max_frag_len: c_int§max_chain_skip: c_int§max_chain_iter: c_int§min_cnt: c_int§min_chain_score: c_int§chain_gap_scale: f32§chain_skip_scale: f32§rmq_size_cap: c_int§rmq_inner_dist: c_int§rmq_rescue_size: c_int§rmq_rescue_ratio: f32§mask_level: f32§mask_len: c_int§pri_ratio: f32§best_n: c_int§alt_drop: f32§a: c_int§b: c_int§q: c_int§e: c_int§q2: c_int§e2: c_int§transition: c_int§sc_ambi: c_int§noncan: c_int§junc_bonus: c_int§junc_pen: c_int§zdrop: c_int§zdrop_inv: c_int§end_bonus: c_int§min_dp_max: c_int§min_ksw_len: c_int§anchor_ext_len: c_int§anchor_ext_shift: c_int§max_clip_ratio: f32§rank_min_len: c_int§rank_frac: f32§pe_ori: c_int§pe_bonus: c_int§jump_min_match: i32§mid_occ_frac: f32§q_occ_frac: f32§min_mid_occ: i32§max_mid_occ: i32§mid_occ: i32§max_occ: i32§max_max_occ: i32§occ_dist: i32§mini_batch_size: i64§max_sw_mat: i64§cap_kalloc: i64§split_prefix: *const c_char

Implementations§

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impl mm_mapopt_t

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pub fn set_no_dual(&mut self)

Set the MM_F_NO_DUAL flag

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pub fn unset_no_dual(&mut self)

Unset the MM_F_NO_DUAL flag

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pub fn set_no_diag(&mut self)

Set the MM_F_NO_DIAG flag

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pub fn unset_no_diag(&mut self)

Unset the MM_F_NO_DIAG flag

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pub fn set_cigar(&mut self)

Set the MM_F_CIGAR flag

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pub fn unset_cigar(&mut self)

Unset the MM_F_CIGAR flag

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pub fn set_out_sam(&mut self)

Set the MM_F_OUT_SAM flag

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pub fn unset_out_sam(&mut self)

Unset the MM_F_OUT_SAM flag

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pub fn set_no_qual(&mut self)

Set the MM_F_NO_QUAL flag

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pub fn unset_no_qual(&mut self)

Unset the MM_F_NO_QUAL flag

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pub fn set_out_cg(&mut self)

Set the MM_F_OUT_CG flag

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pub fn unset_out_cg(&mut self)

Unset the MM_F_OUT_CG flag

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pub fn set_out_cs(&mut self)

Set the MM_F_OUT_CS flag

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pub fn unset_out_cs(&mut self)

Unset the MM_F_OUT_CS flag

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pub fn set_splice(&mut self)

Set the MM_F_SPLICE flag

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pub fn unset_splice(&mut self)

Unset the MM_F_SPLICE flag

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pub fn set_splice_for(&mut self)

Set the MM_F_SPLICE_FOR flag

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pub fn unset_splice_for(&mut self)

Unset the MM_F_SPLICE_FOR flag

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pub fn set_splice_rev(&mut self)

Set the MM_F_SPLICE_REV flag

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pub fn unset_splice_rev(&mut self)

Unset the MM_F_SPLICE_REV flag

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pub fn set_no_ljoin(&mut self)

Set the MM_F_NO_LJOIN flag

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pub fn unset_no_ljoin(&mut self)

Unset the MM_F_NO_LJOIN flag

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pub fn set_out_cs_long(&mut self)

Set the MM_F_OUT_CS_LONG flag

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pub fn unset_out_cs_long(&mut self)

Unset the MM_F_OUT_CS_LONG flag

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pub fn set_sr(&mut self)

Set the MM_F_SR flag

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pub fn unset_sr(&mut self)

Unset the MM_F_SR flag

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pub fn set_frag_mode(&mut self)

Set the MM_F_FRAG_MODE flag

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pub fn unset_frag_mode(&mut self)

Unset the MM_F_FRAG_MODE flag

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pub fn set_no_print_2nd(&mut self)

Set the MM_F_NO_PRINT_2ND flag

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pub fn unset_no_print_2nd(&mut self)

Unset the MM_F_NO_PRINT_2ND flag

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pub fn set_two_io_threads(&mut self)

Set the MM_F_2_IO_THREADS flag

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pub fn unset_two_io_threads(&mut self)

Unset the MM_F_2_IO_THREADS flag

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pub fn set_long_cigar(&mut self)

Set the MM_F_LONG_CIGAR flag

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pub fn unset_long_cigar(&mut self)

Unset the MM_F_LONG_CIGAR flag

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pub fn set_indep_seg(&mut self)

Set the MM_F_INDEPEND_SEG flag

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pub fn unset_indep_seg(&mut self)

Unset the MM_F_INDEPEND_SEG flag

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pub fn set_splice_flank(&mut self)

Set the MM_F_SPLICE_FLANK flag

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pub fn unset_splice_flank(&mut self)

Unset the MM_F_SPLICE_FLANK flag

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pub fn set_softclip(&mut self)

Set the MM_F_SOFTCLIP flag

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pub fn unset_softclip(&mut self)

Unset the MM_F_SOFTCLIP flag

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pub fn set_for_only(&mut self)

Set the MM_F_FOR_ONLY flag

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pub fn unset_for_only(&mut self)

Unset the MM_F_FOR_ONLY flag

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pub fn set_rev_only(&mut self)

Set the MM_F_REV_ONLY flag

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pub fn unset_rev_only(&mut self)

Unset the MM_F_REV_ONLY flag

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pub fn set_heap_sort(&mut self)

Set the MM_F_HEAP_SORT flag

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pub fn unset_heap_sort(&mut self)

Unset the MM_F_HEAP_SORT flag

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pub fn set_all_chains(&mut self)

Set the MM_F_ALL_CHAINS flag

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pub fn unset_all_chains(&mut self)

Unset the MM_F_ALL_CHAINS flag

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pub fn set_out_md(&mut self)

Set the MM_F_OUT_MD flag

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pub fn unset_out_md(&mut self)

Unset the MM_F_OUT_MD flag

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pub fn set_copy_comment(&mut self)

Set the MM_F_COPY_COMMENT flag

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pub fn unset_copy_comment(&mut self)

Unset the MM_F_COPY_COMMENT flag

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pub fn set_eqx(&mut self)

Set the MM_F_EQX flag

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pub fn unset_eqx(&mut self)

Unset the MM_F_EQX flag

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pub fn set_paf_no_hit(&mut self)

Set the MM_F_PAF_NO_HIT flag

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pub fn unset_paf_no_hit(&mut self)

Unset the MM_F_PAF_NO_HIT flag

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pub fn set_no_end_flt(&mut self)

Set the MM_F_NO_END_FLT flag

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pub fn unset_no_end_flt(&mut self)

Unset the MM_F_NO_END_FLT flag

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pub fn set_hard_mlevel(&mut self)

Set the MM_F_HARD_MLEVEL flag

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pub fn unset_hard_mlevel(&mut self)

Unset the MM_F_HARD_MLEVEL flag

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pub fn set_sam_hit_only(&mut self)

Set the MM_F_SAM_HIT_ONLY flag

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pub fn unset_sam_hit_only(&mut self)

Unset the MM_F_SAM_HIT_ONLY flag

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pub fn set_rmq(&mut self)

Set the MM_F_RMQ flag

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pub fn unset_rmq(&mut self)

Unset the MM_F_RMQ flag

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pub fn set_qstrand(&mut self)

Set the MM_F_QSTRAND flag

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pub fn unset_qstrand(&mut self)

Unset the MM_F_QSTRAND flag

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pub fn set_no_inv(&mut self)

Set the MM_F_NO_INV flag

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pub fn unset_no_inv(&mut self)

Unset the MM_F_NO_INV flag

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pub fn set_no_hash_name(&mut self)

Set the MM_F_NO_HASH_NAME flag

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pub fn unset_no_hash_name(&mut self)

Unset the MM_F_NO_HASH_NAME flag

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pub fn set_splice_old(&mut self)

Set the MM_F_SPLICE_OLD flag

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pub fn unset_splice_old(&mut self)

Unset the MM_F_SPLICE_OLD flag

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pub fn set_secondary_seq(&mut self)

Set the MM_F_SECONDARY_SEQ flag

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pub fn unset_secondary_seq(&mut self)

Unset the MM_F_SECONDARY_SEQ flag

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pub fn set_out_ds(&mut self)

Set the MM_F_OUT_DS flag

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pub fn unset_out_ds(&mut self)

Unset the MM_F_OUT_DS flag

Trait Implementations§

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impl Clone for mm_mapopt_t

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fn clone(&self) -> mm_mapopt_t

Returns a duplicate of the value. Read more
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fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source. Read more
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impl Debug for mm_mapopt_t

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fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter. Read more
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impl Default for mm_mapopt_t

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fn default() -> Self

Returns the “default value” for a type. Read more
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impl Copy for mm_mapopt_t

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impl Send for mm_mapopt_t

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impl<T> Any for T
where T: 'static + ?Sized,

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fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more
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impl<T> Borrow<T> for T
where T: ?Sized,

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fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more
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impl<T> BorrowMut<T> for T
where T: ?Sized,

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fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more
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impl<T> CloneToUninit for T
where T: Clone,

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unsafe fn clone_to_uninit(&self, dest: *mut u8)

🔬This is a nightly-only experimental API. (clone_to_uninit)
Performs copy-assignment from self to dest. Read more
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impl<T> From<T> for T

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fn from(t: T) -> T

Returns the argument unchanged.

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impl<T, U> Into<U> for T
where U: From<T>,

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fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

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impl<T> ToOwned for T
where T: Clone,

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type Owned = T

The resulting type after obtaining ownership.
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fn to_owned(&self) -> T

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fn clone_into(&self, target: &mut T)

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impl<T, U> TryFrom<U> for T
where U: Into<T>,

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type Error = Infallible

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fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

Performs the conversion.
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impl<T, U> TryInto<U> for T
where U: TryFrom<T>,

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type Error = <U as TryFrom<T>>::Error

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fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

Performs the conversion.