Structs§
- _wavefront_
aligner_ t - affine2p_
penalties_ t - affine_
penalties_ t - alignment_
form_ t - alignment_
system_ t - bt_
block_ t - cigar_t
- heatmap_
t - linear_
penalties_ t - mm_
allocator_ t - profiler_
counter_ t - profiler_
timer_ t - vector_
t - wavefront_
align_ status_ t - wavefront_
aligner_ attr_ t - wavefront_
bialigner_ t - wavefront_
components_ t - wavefront_
heuristic_ t - wavefront_
penalties_ t - wavefront_
plot_ attr_ t - wavefront_
plot_ t - wavefront_
pos_ t - wavefront_
sequences_ t - wavefront_
slab_ t - wavefront_
t - wf_
backtrace_ buffer_ t
Constants§
- affine2p_
matrix_ type_ affine2p_ matrix_ D1 - affine2p_
matrix_ type_ affine2p_ matrix_ D2 - affine2p_
matrix_ type_ affine2p_ matrix_ I1 - affine2p_
matrix_ type_ affine2p_ matrix_ I2 - affine2p_
matrix_ type_ affine2p_ matrix_ M - alignment_
scope_ t_ compute_ alignment - alignment_
scope_ t_ compute_ score - alignment_
span_ t_ alignment_ end2end - alignment_
span_ t_ alignment_ endsfree - distance_
metric_ t_ edit - distance_
metric_ t_ gap_ affine - distance_
metric_ t_ gap_ affine_ 2p - distance_
metric_ t_ gap_ linear - distance_
metric_ t_ indel - heatmap_
type_ heatmap_ max - heatmap_
type_ heatmap_ min - heatmap_
type_ heatmap_ value - wavefront_
align_ mode_ t_ wf_ align_ biwfa - wavefront_
align_ mode_ t_ wf_ align_ biwfa_ breakpoint_ forward - wavefront_
align_ mode_ t_ wf_ align_ biwfa_ breakpoint_ reverse - wavefront_
align_ mode_ t_ wf_ align_ biwfa_ subsidiary - wavefront_
align_ mode_ t_ wf_ align_ regular - wavefront_
memory_ t_ wavefront_ memory_ high - wavefront_
memory_ t_ wavefront_ memory_ low - wavefront_
memory_ t_ wavefront_ memory_ med - wavefront_
memory_ t_ wavefront_ memory_ ultralow - wavefront_
status_ type_ wavefront_ status_ busy - wavefront_
status_ type_ wavefront_ status_ deallocated - wavefront_
status_ type_ wavefront_ status_ free - wf_
heuristic_ strategy_ wf_ heuristic_ banded_ adaptive - wf_
heuristic_ strategy_ wf_ heuristic_ banded_ static - wf_
heuristic_ strategy_ wf_ heuristic_ none - wf_
heuristic_ strategy_ wf_ heuristic_ wfadaptive - wf_
heuristic_ strategy_ wf_ heuristic_ wfmash - wf_
heuristic_ strategy_ wf_ heuristic_ xdrop - wf_
heuristic_ strategy_ wf_ heuristic_ zdrop - wf_
sequences_ mode_ t_ wf_ sequences_ ascii - wf_
sequences_ mode_ t_ wf_ sequences_ lambda - wf_
sequences_ mode_ t_ wf_ sequences_ packed2bits - wf_
slab_ mode_ t_ wf_ slab_ reuse - wf_
slab_ mode_ t_ wf_ slab_ tight
Statics§
Functions§
- wavefront_
align ⚠ - wavefront_
align_ ⚠lambda - wavefront_
align_ ⚠packed2bits - wavefront_
align_ ⚠strerror - wavefront_
align_ ⚠strerror_ short - wavefront_
aligner_ ⚠delete - wavefront_
aligner_ ⚠get_ size - wavefront_
aligner_ ⚠init - wavefront_
aligner_ ⚠maxtrim_ cigar - wavefront_
aligner_ ⚠new - wavefront_
aligner_ ⚠print - wavefront_
aligner_ ⚠print_ conf - wavefront_
aligner_ ⚠print_ mode - wavefront_
aligner_ ⚠print_ scope - wavefront_
aligner_ ⚠reap - wavefront_
aligner_ ⚠set_ alignment_ end_ to_ end - wavefront_
aligner_ ⚠set_ alignment_ extension - wavefront_
aligner_ ⚠set_ alignment_ free_ ends - wavefront_
aligner_ ⚠set_ heuristic_ banded_ adaptive - wavefront_
aligner_ ⚠set_ heuristic_ banded_ static - wavefront_
aligner_ ⚠set_ heuristic_ none - wavefront_
aligner_ ⚠set_ heuristic_ wfadaptive - wavefront_
aligner_ ⚠set_ heuristic_ wfmash - wavefront_
aligner_ ⚠set_ heuristic_ xdrop - wavefront_
aligner_ ⚠set_ heuristic_ zdrop - wavefront_
aligner_ ⚠set_ max_ alignment_ steps - wavefront_
aligner_ ⚠set_ max_ memory - wavefront_
aligner_ ⚠set_ max_ num_ threads - wavefront_
aligner_ ⚠set_ min_ offsets_ per_ thread - wavefront_
allocate ⚠ - wavefront_
bialigner_ ⚠delete - wavefront_
bialigner_ ⚠get_ size - wavefront_
bialigner_ ⚠new - wavefront_
bialigner_ ⚠reap - wavefront_
bialigner_ ⚠set_ heuristic - wavefront_
bialigner_ ⚠set_ max_ alignment_ steps - wavefront_
bialigner_ ⚠set_ max_ memory - wavefront_
bialigner_ ⚠set_ max_ num_ threads - wavefront_
bialigner_ ⚠set_ min_ offsets_ per_ thread - wavefront_
bialigner_ ⚠set_ sequences_ ascii - wavefront_
bialigner_ ⚠set_ sequences_ bounds - wavefront_
bialigner_ ⚠set_ sequences_ lambda - wavefront_
bialigner_ ⚠set_ sequences_ packed2bits - wavefront_
components_ ⚠allocate - wavefront_
components_ ⚠clear - wavefront_
components_ ⚠compact_ bt_ buffer - wavefront_
components_ ⚠free - wavefront_
components_ ⚠reap - wavefront_
components_ ⚠resize - wavefront_
components_ ⚠resize_ null__ victim - wavefront_
free ⚠ - wavefront_
get_ ⚠size - wavefront_
heuristic_ ⚠clear - wavefront_
heuristic_ ⚠cufoff - wavefront_
heuristic_ ⚠print - wavefront_
heuristic_ ⚠set_ banded_ adaptive - wavefront_
heuristic_ ⚠set_ banded_ static - wavefront_
heuristic_ ⚠set_ none - wavefront_
heuristic_ ⚠set_ wfadaptive - wavefront_
heuristic_ ⚠set_ wfmash - wavefront_
heuristic_ ⚠set_ xdrop - wavefront_
heuristic_ ⚠set_ zdrop - wavefront_
init ⚠ - wavefront_
init_ ⚠null - wavefront_
init_ ⚠victim - wavefront_
penalties_ ⚠print - wavefront_
penalties_ ⚠set_ affine - wavefront_
penalties_ ⚠set_ affine2p - wavefront_
penalties_ ⚠set_ edit - wavefront_
penalties_ ⚠set_ indel - wavefront_
penalties_ ⚠set_ linear - wavefront_
plot ⚠ - wavefront_
plot_ ⚠delete - wavefront_
plot_ ⚠new - wavefront_
plot_ ⚠print - wavefront_
plot_ ⚠resize - wavefront_
resize ⚠ - wavefront_
sequences_ ⚠allocate - wavefront_
sequences_ ⚠cmp - wavefront_
sequences_ ⚠free - wavefront_
sequences_ ⚠get_ pattern - wavefront_
sequences_ ⚠get_ text - wavefront_
sequences_ ⚠init_ ascii - wavefront_
sequences_ ⚠init_ lambda - wavefront_
sequences_ ⚠init_ packed2bits - wavefront_
sequences_ ⚠set_ bounds - wavefront_
set_ ⚠limits - wavefront_
slab_ ⚠allocate - wavefront_
slab_ ⚠clear - wavefront_
slab_ ⚠delete - wavefront_
slab_ ⚠free - wavefront_
slab_ ⚠get_ size - wavefront_
slab_ ⚠new - wavefront_
slab_ ⚠reap - wavefront_
slab_ ⚠set_ mode
Type Aliases§
- FILE
- __
off64_ t - __off_t
- __
syscall_ slong_ t - __
time_ t - affine2p_
matrix_ type - alignment_
match_ funct_ t - alignment_
scope_ t - alignment_
span_ t - bt_
block_ idx_ t - distance_
metric_ t - heatmap_
type - pcigar_
t - timespec
- wavefront_
align_ mode_ t - wavefront_
aligner_ t - wavefront_
memory_ t - wavefront_
status_ type - wf_
heuristic_ strategy - wf_
offset_ t - wf_
sequences_ mode_ t - wf_
slab_ mode_ t