minimap2 0.2.30.3 → 1.2.31.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/README.md +48 -63
- data/ext/minimap2/Makefile +1 -1
- data/ext/minimap2/format.c +12 -2
- data/ext/minimap2/hit.c +19 -8
- data/ext/minimap2/ksw2_ll_sse.c +2 -2
- data/ext/minimap2/minimap.h +2 -1
- data/ext/minimap2/pe.c +7 -2
- data/ext/ruby_minimap2/extconf.rb +47 -0
- data/ext/ruby_minimap2/native_main.c +15 -0
- data/ext/ruby_minimap2/ruby_minimap2.c +1134 -0
- data/lib/minimap2/aligner.rb +66 -374
- data/lib/minimap2/alignment.rb +22 -11
- data/lib/minimap2/version.rb +2 -1
- data/lib/minimap2.rb +39 -110
- metadata +8 -89
- data/ext/Rakefile +0 -60
- data/ext/cmappy/cmappy.c +0 -134
- data/ext/cmappy/cmappy.h +0 -46
- data/ext/minimap2/FAQ.md +0 -46
- data/ext/minimap2/MANIFEST.in +0 -10
- data/ext/minimap2/Makefile.simde +0 -97
- data/ext/minimap2/NEWS.md +0 -989
- data/ext/minimap2/README.md +0 -428
- data/ext/minimap2/code_of_conduct.md +0 -30
- data/ext/minimap2/cookbook.md +0 -243
- data/ext/minimap2/minimap2.1 +0 -844
- data/ext/minimap2/misc/README.md +0 -180
- data/ext/minimap2/misc/pafcluster.js +0 -241
- data/ext/minimap2/misc/paftools.js +0 -3734
- data/ext/minimap2/pyproject.toml +0 -2
- data/ext/minimap2/python/README.rst +0 -198
- data/ext/minimap2/python/cmappy.h +0 -152
- data/ext/minimap2/python/cmappy.pxd +0 -156
- data/ext/minimap2/python/mappy.pyx +0 -289
- data/ext/minimap2/python/minimap2.py +0 -41
- data/ext/minimap2/setup.py +0 -55
- data/ext/minimap2/test/MT-human.fa +0 -278
- data/ext/minimap2/test/MT-orang.fa +0 -276
- data/ext/minimap2/test/q-inv.fa +0 -4
- data/ext/minimap2/test/q2.fa +0 -2
- data/ext/minimap2/test/t-inv.fa +0 -127
- data/ext/minimap2/test/t2.fa +0 -2
- data/ext/minimap2/test/x3s-aln.txt +0 -5
- data/ext/minimap2/test/x3s-qry.fa +0 -5
- data/ext/minimap2/test/x3s-ref.fa +0 -10
- data/ext/minimap2/tex/Makefile +0 -21
- data/ext/minimap2/tex/bioinfo.cls +0 -930
- data/ext/minimap2/tex/blasr-mc.eval +0 -17
- data/ext/minimap2/tex/bowtie2-s3.sam.eval +0 -28
- data/ext/minimap2/tex/bwa-s3.sam.eval +0 -52
- data/ext/minimap2/tex/bwa.eval +0 -55
- data/ext/minimap2/tex/eval2roc.pl +0 -33
- data/ext/minimap2/tex/graphmap.eval +0 -4
- data/ext/minimap2/tex/hs38-simu.sh +0 -10
- data/ext/minimap2/tex/minialign.eval +0 -49
- data/ext/minimap2/tex/minimap2.bib +0 -460
- data/ext/minimap2/tex/minimap2.tex +0 -724
- data/ext/minimap2/tex/mm2-s3.sam.eval +0 -62
- data/ext/minimap2/tex/mm2-update.tex +0 -240
- data/ext/minimap2/tex/mm2.approx.eval +0 -12
- data/ext/minimap2/tex/mm2.eval +0 -13
- data/ext/minimap2/tex/natbib.bst +0 -1288
- data/ext/minimap2/tex/natbib.sty +0 -803
- data/ext/minimap2/tex/ngmlr.eval +0 -38
- data/ext/minimap2/tex/roc.gp +0 -60
- data/ext/minimap2/tex/snap-s3.sam.eval +0 -62
- data/ext/minimap2.patch +0 -19
- data/lib/minimap2/ffi/constants.rb +0 -267
- data/lib/minimap2/ffi/functions.rb +0 -239
- data/lib/minimap2/ffi/mappy.rb +0 -104
- data/lib/minimap2/ffi.rb +0 -27
|
@@ -1,289 +0,0 @@
|
|
|
1
|
-
from libc.stdint cimport uint8_t, int8_t
|
|
2
|
-
from libc.stdlib cimport free
|
|
3
|
-
cimport cmappy
|
|
4
|
-
import sys
|
|
5
|
-
|
|
6
|
-
__version__ = '2.30'
|
|
7
|
-
|
|
8
|
-
cmappy.mm_reset_timer()
|
|
9
|
-
|
|
10
|
-
cdef class Alignment:
|
|
11
|
-
cdef int _ctg_len, _r_st, _r_en
|
|
12
|
-
cdef int _q_st, _q_en
|
|
13
|
-
cdef int _NM, _mlen, _blen
|
|
14
|
-
cdef int8_t _strand, _trans_strand
|
|
15
|
-
cdef uint8_t _mapq, _is_primary
|
|
16
|
-
cdef int _seg_id
|
|
17
|
-
cdef _ctg, _cigar, _cs, _MD # these are python objects
|
|
18
|
-
|
|
19
|
-
def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, mlen, blen, NM, trans_strand, seg_id, cs_str, MD_str):
|
|
20
|
-
self._ctg = ctg if isinstance(ctg, str) else ctg.decode()
|
|
21
|
-
self._ctg_len, self._r_st, self._r_en = cl, cs, ce
|
|
22
|
-
self._strand, self._q_st, self._q_en = strand, qs, qe
|
|
23
|
-
self._NM, self._mlen, self._blen = NM, mlen, blen
|
|
24
|
-
self._mapq = mapq
|
|
25
|
-
self._cigar = cigar
|
|
26
|
-
self._is_primary = is_primary
|
|
27
|
-
self._trans_strand = trans_strand
|
|
28
|
-
self._seg_id = seg_id
|
|
29
|
-
self._cs = cs_str
|
|
30
|
-
self._MD = MD_str
|
|
31
|
-
|
|
32
|
-
@property
|
|
33
|
-
def ctg(self): return self._ctg
|
|
34
|
-
|
|
35
|
-
@property
|
|
36
|
-
def ctg_len(self): return self._ctg_len
|
|
37
|
-
|
|
38
|
-
@property
|
|
39
|
-
def r_st(self): return self._r_st
|
|
40
|
-
|
|
41
|
-
@property
|
|
42
|
-
def r_en(self): return self._r_en
|
|
43
|
-
|
|
44
|
-
@property
|
|
45
|
-
def strand(self): return self._strand
|
|
46
|
-
|
|
47
|
-
@property
|
|
48
|
-
def trans_strand(self): return self._trans_strand
|
|
49
|
-
|
|
50
|
-
@property
|
|
51
|
-
def blen(self): return self._blen
|
|
52
|
-
|
|
53
|
-
@property
|
|
54
|
-
def mlen(self): return self._mlen
|
|
55
|
-
|
|
56
|
-
@property
|
|
57
|
-
def NM(self): return self._NM
|
|
58
|
-
|
|
59
|
-
@property
|
|
60
|
-
def is_primary(self): return (self._is_primary != 0)
|
|
61
|
-
|
|
62
|
-
@property
|
|
63
|
-
def q_st(self): return self._q_st
|
|
64
|
-
|
|
65
|
-
@property
|
|
66
|
-
def q_en(self): return self._q_en
|
|
67
|
-
|
|
68
|
-
@property
|
|
69
|
-
def mapq(self): return self._mapq
|
|
70
|
-
|
|
71
|
-
@property
|
|
72
|
-
def cigar(self): return self._cigar
|
|
73
|
-
|
|
74
|
-
@property
|
|
75
|
-
def read_num(self): return self._seg_id + 1
|
|
76
|
-
|
|
77
|
-
@property
|
|
78
|
-
def cs(self): return self._cs
|
|
79
|
-
|
|
80
|
-
@property
|
|
81
|
-
def MD(self): return self._MD
|
|
82
|
-
|
|
83
|
-
@property
|
|
84
|
-
def cigar_str(self):
|
|
85
|
-
return "".join(map(lambda x: str(x[0]) + 'MIDNSHP=XB'[x[1]], self._cigar))
|
|
86
|
-
|
|
87
|
-
def __str__(self):
|
|
88
|
-
if self._strand > 0: strand = '+'
|
|
89
|
-
elif self._strand < 0: strand = '-'
|
|
90
|
-
else: strand = '?'
|
|
91
|
-
if self._is_primary != 0: tp = 'tp:A:P'
|
|
92
|
-
else: tp = 'tp:A:S'
|
|
93
|
-
if self._trans_strand > 0: ts = 'ts:A:+'
|
|
94
|
-
elif self._trans_strand < 0: ts = 'ts:A:-'
|
|
95
|
-
else: ts = 'ts:A:.'
|
|
96
|
-
a = [str(self._q_st), str(self._q_en), strand, self._ctg, str(self._ctg_len), str(self._r_st), str(self._r_en),
|
|
97
|
-
str(self._mlen), str(self._blen), str(self._mapq), tp, ts, "cg:Z:" + self.cigar_str]
|
|
98
|
-
if self._cs != "": a.append("cs:Z:" + self._cs)
|
|
99
|
-
if self._MD != "": a.append("MD:Z:" + self._MD)
|
|
100
|
-
return "\t".join(a)
|
|
101
|
-
|
|
102
|
-
cdef class ThreadBuffer:
|
|
103
|
-
cdef cmappy.mm_tbuf_t *_b
|
|
104
|
-
|
|
105
|
-
def __cinit__(self):
|
|
106
|
-
self._b = cmappy.mm_tbuf_init()
|
|
107
|
-
|
|
108
|
-
def __dealloc__(self):
|
|
109
|
-
cmappy.mm_tbuf_destroy(self._b)
|
|
110
|
-
|
|
111
|
-
cdef class Aligner:
|
|
112
|
-
cdef cmappy.mm_idx_t *_idx
|
|
113
|
-
cdef cmappy.mm_idxopt_t idx_opt
|
|
114
|
-
cdef cmappy.mm_mapopt_t map_opt
|
|
115
|
-
|
|
116
|
-
def __cinit__(self, fn_idx_in=None, preset=None, k=None, w=None, min_cnt=None, min_chain_score=None, min_dp_score=None, bw=None, bw_long=None, best_n=None, n_threads=3, fn_idx_out=None, max_frag_len=None, extra_flags=None, seq=None, scoring=None, sc_ambi=None, max_chain_skip=None):
|
|
117
|
-
self._idx = NULL
|
|
118
|
-
cmappy.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
|
|
119
|
-
if preset is not None:
|
|
120
|
-
cmappy.mm_set_opt(str.encode(preset), &self.idx_opt, &self.map_opt) # apply preset
|
|
121
|
-
self.map_opt.flag |= 4 # always perform alignment
|
|
122
|
-
self.idx_opt.batch_size = 0x7fffffffffffffffL # always build a uni-part index
|
|
123
|
-
if k is not None: self.idx_opt.k = k
|
|
124
|
-
if w is not None: self.idx_opt.w = w
|
|
125
|
-
if min_cnt is not None: self.map_opt.min_cnt = min_cnt
|
|
126
|
-
if min_chain_score is not None: self.map_opt.min_chain_score = min_chain_score
|
|
127
|
-
if min_dp_score is not None: self.map_opt.min_dp_max = min_dp_score
|
|
128
|
-
if bw is not None: self.map_opt.bw = bw
|
|
129
|
-
if bw_long is not None: self.map_opt.bw_long = bw_long
|
|
130
|
-
if best_n is not None: self.map_opt.best_n = best_n
|
|
131
|
-
if max_frag_len is not None: self.map_opt.max_frag_len = max_frag_len
|
|
132
|
-
if extra_flags is not None: self.map_opt.flag |= extra_flags
|
|
133
|
-
if scoring is not None and len(scoring) >= 4:
|
|
134
|
-
self.map_opt.a, self.map_opt.b = scoring[0], scoring[1]
|
|
135
|
-
self.map_opt.q, self.map_opt.e = scoring[2], scoring[3]
|
|
136
|
-
self.map_opt.q2, self.map_opt.e2 = self.map_opt.q, self.map_opt.e
|
|
137
|
-
if len(scoring) >= 6:
|
|
138
|
-
self.map_opt.q2, self.map_opt.e2 = scoring[4], scoring[5]
|
|
139
|
-
if len(scoring) >= 7:
|
|
140
|
-
self.map_opt.sc_ambi = scoring[6]
|
|
141
|
-
if sc_ambi is not None: self.map_opt.sc_ambi = sc_ambi
|
|
142
|
-
if max_chain_skip is not None: self.map_opt.max_chain_skip = max_chain_skip
|
|
143
|
-
|
|
144
|
-
cdef cmappy.mm_idx_reader_t *r;
|
|
145
|
-
|
|
146
|
-
if seq is None:
|
|
147
|
-
if fn_idx_out is None:
|
|
148
|
-
r = cmappy.mm_idx_reader_open(str.encode(fn_idx_in), &self.idx_opt, NULL)
|
|
149
|
-
else:
|
|
150
|
-
r = cmappy.mm_idx_reader_open(str.encode(fn_idx_in), &self.idx_opt, str.encode(fn_idx_out))
|
|
151
|
-
if r is not NULL:
|
|
152
|
-
self._idx = cmappy.mm_idx_reader_read(r, n_threads) # NB: ONLY read the first part
|
|
153
|
-
cmappy.mm_idx_reader_close(r)
|
|
154
|
-
cmappy.mm_mapopt_update(&self.map_opt, self._idx)
|
|
155
|
-
cmappy.mm_idx_index_name(self._idx)
|
|
156
|
-
else:
|
|
157
|
-
self._idx = cmappy.mappy_idx_seq(self.idx_opt.w, self.idx_opt.k, self.idx_opt.flag&1, self.idx_opt.bucket_bits, str.encode(seq), len(seq))
|
|
158
|
-
cmappy.mm_mapopt_update(&self.map_opt, self._idx)
|
|
159
|
-
self.map_opt.mid_occ = 1000 # don't filter high-occ seeds
|
|
160
|
-
|
|
161
|
-
def __dealloc__(self):
|
|
162
|
-
if self._idx is not NULL:
|
|
163
|
-
cmappy.mm_idx_destroy(self._idx)
|
|
164
|
-
|
|
165
|
-
def __bool__(self):
|
|
166
|
-
return (self._idx != NULL)
|
|
167
|
-
|
|
168
|
-
def map(self, seq, seq2=None, name=None, buf=None, cs=False, MD=False, max_frag_len=None, extra_flags=None):
|
|
169
|
-
cdef cmappy.mm_reg1_t *regs
|
|
170
|
-
cdef cmappy.mm_hitpy_t h
|
|
171
|
-
cdef ThreadBuffer b
|
|
172
|
-
cdef int n_regs
|
|
173
|
-
cdef char *cs_str = NULL
|
|
174
|
-
cdef int l_cs_str, m_cs_str = 0
|
|
175
|
-
cdef void *km
|
|
176
|
-
cdef cmappy.mm_mapopt_t map_opt
|
|
177
|
-
|
|
178
|
-
if self._idx == NULL: return
|
|
179
|
-
if ((self.map_opt.flag & 4) and (self._idx.flag & 2)): return
|
|
180
|
-
map_opt = self.map_opt
|
|
181
|
-
if max_frag_len is not None: map_opt.max_frag_len = max_frag_len
|
|
182
|
-
if extra_flags is not None: map_opt.flag |= extra_flags
|
|
183
|
-
|
|
184
|
-
if self._idx is NULL: return None
|
|
185
|
-
if buf is None: b = ThreadBuffer()
|
|
186
|
-
else: b = buf
|
|
187
|
-
km = cmappy.mm_tbuf_get_km(b._b)
|
|
188
|
-
|
|
189
|
-
_seq = seq if isinstance(seq, bytes) else seq.encode()
|
|
190
|
-
if name is not None:
|
|
191
|
-
_name = name if isinstance(name, bytes) else name.encode()
|
|
192
|
-
|
|
193
|
-
if seq2 is None:
|
|
194
|
-
if name is None:
|
|
195
|
-
regs = cmappy.mm_map_aux(self._idx, NULL, _seq, NULL, &n_regs, b._b, &map_opt)
|
|
196
|
-
else:
|
|
197
|
-
regs = cmappy.mm_map_aux(self._idx, _name, _seq, NULL, &n_regs, b._b, &map_opt)
|
|
198
|
-
else:
|
|
199
|
-
_seq2 = seq2 if isinstance(seq2, bytes) else seq2.encode()
|
|
200
|
-
if name is None:
|
|
201
|
-
regs = cmappy.mm_map_aux(self._idx, NULL, _seq, _seq2, &n_regs, b._b, &map_opt)
|
|
202
|
-
else:
|
|
203
|
-
regs = cmappy.mm_map_aux(self._idx, _name, _seq, _seq2, &n_regs, b._b, &map_opt)
|
|
204
|
-
|
|
205
|
-
try:
|
|
206
|
-
i = 0
|
|
207
|
-
while i < n_regs:
|
|
208
|
-
cmappy.mm_reg2hitpy(self._idx, ®s[i], &h)
|
|
209
|
-
cigar, _cs, _MD = [], '', ''
|
|
210
|
-
for k in range(h.n_cigar32): # convert the 32-bit CIGAR encoding to Python array
|
|
211
|
-
c = h.cigar32[k]
|
|
212
|
-
cigar.append([c>>4, c&0xf])
|
|
213
|
-
if cs or MD: # generate the cs and/or the MD tag, if requested
|
|
214
|
-
_cur_seq = _seq2 if h.seg_id > 0 and seq2 is not None else _seq
|
|
215
|
-
if cs:
|
|
216
|
-
l_cs_str = cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, ®s[i], _cur_seq, 1)
|
|
217
|
-
_cs = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
|
|
218
|
-
if MD:
|
|
219
|
-
l_cs_str = cmappy.mm_gen_MD(km, &cs_str, &m_cs_str, self._idx, ®s[i], _cur_seq)
|
|
220
|
-
_MD = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
|
|
221
|
-
yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.mlen, h.blen, h.NM, h.trans_strand, h.seg_id, _cs, _MD)
|
|
222
|
-
cmappy.mm_free_reg1(®s[i])
|
|
223
|
-
i += 1
|
|
224
|
-
finally:
|
|
225
|
-
while i < n_regs:
|
|
226
|
-
cmappy.mm_free_reg1(®s[i])
|
|
227
|
-
i += 1
|
|
228
|
-
free(regs)
|
|
229
|
-
free(cs_str)
|
|
230
|
-
|
|
231
|
-
def seq(self, str name, int start=0, int end=0x7fffffff):
|
|
232
|
-
cdef int l
|
|
233
|
-
cdef char *s
|
|
234
|
-
if self._idx == NULL: return
|
|
235
|
-
if ((self.map_opt.flag & 4) and (self._idx.flag & 2)): return
|
|
236
|
-
s = cmappy.mappy_fetch_seq(self._idx, name.encode(), start, end, &l)
|
|
237
|
-
if l == 0: return None
|
|
238
|
-
r = s[:l] if isinstance(s, str) else s[:l].decode()
|
|
239
|
-
free(s)
|
|
240
|
-
return r
|
|
241
|
-
|
|
242
|
-
@property
|
|
243
|
-
def k(self): return self._idx.k
|
|
244
|
-
|
|
245
|
-
@property
|
|
246
|
-
def w(self): return self._idx.w
|
|
247
|
-
|
|
248
|
-
@property
|
|
249
|
-
def n_seq(self): return self._idx.n_seq
|
|
250
|
-
|
|
251
|
-
@property
|
|
252
|
-
def seq_names(self):
|
|
253
|
-
cdef char *p
|
|
254
|
-
if self._idx == NULL: return
|
|
255
|
-
sn = []
|
|
256
|
-
for i in range(self._idx.n_seq):
|
|
257
|
-
p = self._idx.seq[i].name
|
|
258
|
-
s = p if isinstance(p, str) else p.decode()
|
|
259
|
-
sn.append(s)
|
|
260
|
-
return sn
|
|
261
|
-
|
|
262
|
-
def fastx_read(fn, read_comment=False):
|
|
263
|
-
cdef cmappy.kseq_t *ks
|
|
264
|
-
ks = cmappy.mm_fastx_open(str.encode(fn))
|
|
265
|
-
if ks is NULL: return None
|
|
266
|
-
while cmappy.kseq_read(ks) >= 0:
|
|
267
|
-
if ks.qual.l > 0: qual = ks.qual.s if isinstance(ks.qual.s, str) else ks.qual.s.decode()
|
|
268
|
-
else: qual = None
|
|
269
|
-
name = ks.name.s if isinstance(ks.name.s, str) else ks.name.s.decode()
|
|
270
|
-
seq = ks.seq.s if isinstance(ks.seq.s, str) else ks.seq.s.decode()
|
|
271
|
-
if read_comment:
|
|
272
|
-
if ks.comment.l > 0: comment = ks.comment.s if isinstance(ks.comment.s, str) else ks.comment.s.decode()
|
|
273
|
-
else: comment = None
|
|
274
|
-
yield name, seq, qual, comment
|
|
275
|
-
else:
|
|
276
|
-
yield name, seq, qual
|
|
277
|
-
cmappy.mm_fastx_close(ks)
|
|
278
|
-
|
|
279
|
-
def revcomp(seq):
|
|
280
|
-
l = len(seq)
|
|
281
|
-
bseq = seq if isinstance(seq, bytes) else seq.encode()
|
|
282
|
-
cdef char *s = cmappy.mappy_revcomp(l, bseq)
|
|
283
|
-
r = s[:l] if isinstance(s, str) else s[:l].decode()
|
|
284
|
-
free(s)
|
|
285
|
-
return r
|
|
286
|
-
|
|
287
|
-
def verbose(v=None):
|
|
288
|
-
if v is None: v = -1
|
|
289
|
-
return cmappy.mm_verbose_level(v)
|
|
@@ -1,41 +0,0 @@
|
|
|
1
|
-
#!/usr/bin/env python
|
|
2
|
-
|
|
3
|
-
import sys
|
|
4
|
-
import getopt
|
|
5
|
-
import mappy as mp
|
|
6
|
-
|
|
7
|
-
def main(argv):
|
|
8
|
-
opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:cM")
|
|
9
|
-
if len(args) < 2:
|
|
10
|
-
print("Usage: minimap2.py [options] <ref.fa>|<ref.mmi> <query.fq>")
|
|
11
|
-
print("Options:")
|
|
12
|
-
print(" -x STR preset: sr, map-pb, map-ont, asm5, asm10 or splice")
|
|
13
|
-
print(" -n INT mininum number of minimizers")
|
|
14
|
-
print(" -m INT mininum chaining score")
|
|
15
|
-
print(" -k INT k-mer length")
|
|
16
|
-
print(" -w INT minimizer window length")
|
|
17
|
-
print(" -r INT band width")
|
|
18
|
-
print(" -c output the cs tag")
|
|
19
|
-
print(" -M output the MD tag")
|
|
20
|
-
sys.exit(1)
|
|
21
|
-
|
|
22
|
-
preset = min_cnt = min_sc = k = w = bw = None
|
|
23
|
-
out_cs = out_MD = False
|
|
24
|
-
for opt, arg in opts:
|
|
25
|
-
if opt == '-x': preset = arg
|
|
26
|
-
elif opt == '-n': min_cnt = int(arg)
|
|
27
|
-
elif opt == '-m': min_chain_score = int(arg)
|
|
28
|
-
elif opt == '-r': bw = int(arg)
|
|
29
|
-
elif opt == '-k': k = int(arg)
|
|
30
|
-
elif opt == '-w': w = int(arg)
|
|
31
|
-
elif opt == '-c': out_cs = True
|
|
32
|
-
elif opt == '-M': out_MD = True
|
|
33
|
-
|
|
34
|
-
a = mp.Aligner(args[0], preset=preset, min_cnt=min_cnt, min_chain_score=min_sc, k=k, w=w, bw=bw)
|
|
35
|
-
if not a: raise Exception("ERROR: failed to load/build index file '{}'".format(args[0]))
|
|
36
|
-
for name, seq, qual in mp.fastx_read(args[1]): # read one sequence
|
|
37
|
-
for h in a.map(seq, cs=out_cs, MD=out_MD): # traverse hits
|
|
38
|
-
print('{}\t{}\t{}'.format(name, len(seq), h))
|
|
39
|
-
|
|
40
|
-
if __name__ == "__main__":
|
|
41
|
-
main(sys.argv)
|
data/ext/minimap2/setup.py
DELETED
|
@@ -1,55 +0,0 @@
|
|
|
1
|
-
try:
|
|
2
|
-
from setuptools import setup, Extension
|
|
3
|
-
except ImportError:
|
|
4
|
-
from distutils.core import setup
|
|
5
|
-
from distutils.extension import Extension
|
|
6
|
-
|
|
7
|
-
import sys, platform
|
|
8
|
-
|
|
9
|
-
sys.path.append('python')
|
|
10
|
-
|
|
11
|
-
extra_compile_args = ['-DHAVE_KALLOC']
|
|
12
|
-
include_dirs = ["."]
|
|
13
|
-
|
|
14
|
-
if platform.machine() in ["aarch64", "arm64"]:
|
|
15
|
-
include_dirs.append("sse2neon/")
|
|
16
|
-
extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
|
|
17
|
-
else:
|
|
18
|
-
extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
|
|
19
|
-
|
|
20
|
-
def readme():
|
|
21
|
-
with open('python/README.rst') as f:
|
|
22
|
-
return f.read()
|
|
23
|
-
|
|
24
|
-
setup(
|
|
25
|
-
name = 'mappy',
|
|
26
|
-
version = '2.30',
|
|
27
|
-
url = 'https://github.com/lh3/minimap2',
|
|
28
|
-
description = 'Minimap2 python binding',
|
|
29
|
-
long_description = readme(),
|
|
30
|
-
author = 'Heng Li',
|
|
31
|
-
author_email = 'lh3@me.com',
|
|
32
|
-
license = 'MIT',
|
|
33
|
-
keywords = 'sequence-alignment',
|
|
34
|
-
scripts = ['python/minimap2.py'],
|
|
35
|
-
ext_modules = [Extension('mappy',
|
|
36
|
-
sources = ['python/mappy.pyx', 'align.c', 'bseq.c', 'lchain.c', 'seed.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'jump.c', 'options.c',
|
|
37
|
-
'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
|
|
38
|
-
'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c', 'splitidx.c'],
|
|
39
|
-
depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
|
|
40
|
-
'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
|
|
41
|
-
'python/cmappy.h', 'python/cmappy.pxd'],
|
|
42
|
-
extra_compile_args = extra_compile_args,
|
|
43
|
-
include_dirs = include_dirs,
|
|
44
|
-
libraries = ['z', 'm', 'pthread'])],
|
|
45
|
-
classifiers = [
|
|
46
|
-
'Development Status :: 5 - Production/Stable',
|
|
47
|
-
'License :: OSI Approved :: MIT License',
|
|
48
|
-
'Operating System :: POSIX',
|
|
49
|
-
'Programming Language :: C',
|
|
50
|
-
'Programming Language :: Cython',
|
|
51
|
-
'Programming Language :: Python :: 2.7',
|
|
52
|
-
'Programming Language :: Python :: 3',
|
|
53
|
-
'Intended Audience :: Science/Research',
|
|
54
|
-
'Topic :: Scientific/Engineering :: Bio-Informatics'],
|
|
55
|
-
setup_requires=["cython"])
|
|
@@ -1,278 +0,0 @@
|
|
|
1
|
-
>MT_human
|
|
2
|
-
GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT
|
|
3
|
-
CGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC
|
|
4
|
-
GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT
|
|
5
|
-
ACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA
|
|
6
|
-
ACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA
|
|
7
|
-
AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA
|
|
8
|
-
ACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC
|
|
9
|
-
TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAAT
|
|
10
|
-
CTCATCAATACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATA
|
|
11
|
-
CCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA
|
|
12
|
-
GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGGTC
|
|
13
|
-
CTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGT
|
|
14
|
-
TCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGCAATGCAGCTC
|
|
15
|
-
AAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA
|
|
16
|
-
ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC
|
|
17
|
-
GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCC
|
|
18
|
-
TCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGAC
|
|
19
|
-
TACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTAGA
|
|
20
|
-
TACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAA
|
|
21
|
-
CACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG
|
|
22
|
-
AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA
|
|
23
|
-
CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAG
|
|
24
|
-
ACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAG
|
|
25
|
-
AAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAG
|
|
26
|
-
AGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC
|
|
27
|
-
AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAAGT
|
|
28
|
-
CGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACACA
|
|
29
|
-
AAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA
|
|
30
|
-
GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAA
|
|
31
|
-
AGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG
|
|
32
|
-
AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAA
|
|
33
|
-
TTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAGCT
|
|
34
|
-
ACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATA
|
|
35
|
-
GGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAG
|
|
36
|
-
TTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC
|
|
37
|
-
CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTA
|
|
38
|
-
ACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCA
|
|
39
|
-
CTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATC
|
|
40
|
-
ACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGC
|
|
41
|
-
CTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC
|
|
42
|
-
AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAAAA
|
|
43
|
-
AAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC
|
|
44
|
-
ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCT
|
|
45
|
-
AACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCC
|
|
46
|
-
ACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCG
|
|
47
|
-
GGCATAACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAGTA
|
|
48
|
-
CCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGCGA
|
|
49
|
-
CCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAA
|
|
50
|
-
CTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA
|
|
51
|
-
GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA
|
|
52
|
-
GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTAC
|
|
53
|
-
GTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACaTTCAAATTCCTCC
|
|
54
|
-
CTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAATGA
|
|
55
|
-
TATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATGGC
|
|
56
|
-
AGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTCTT
|
|
57
|
-
AACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA
|
|
58
|
-
TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAAC
|
|
59
|
-
GTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAA
|
|
60
|
-
GAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCT
|
|
61
|
-
CTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC
|
|
62
|
-
AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTGA
|
|
63
|
-
TCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCAA
|
|
64
|
-
ACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC
|
|
65
|
-
TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCA
|
|
66
|
-
TGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTC
|
|
67
|
-
GACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGC
|
|
68
|
-
CCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCACC
|
|
69
|
-
ACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACATAT
|
|
70
|
-
TTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCC
|
|
71
|
-
CGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA
|
|
72
|
-
GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACC
|
|
73
|
-
TAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCC
|
|
74
|
-
CCTTATTTCTAGGACTATGAGAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCC
|
|
75
|
-
ACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCG
|
|
76
|
-
AAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTACT
|
|
77
|
-
CTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTGAG
|
|
78
|
-
TAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC
|
|
79
|
-
GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTC
|
|
80
|
-
TAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCA
|
|
81
|
-
ATCAATACTCATCATTAATAATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCT
|
|
82
|
-
TTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCTTC
|
|
83
|
-
TCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAAATCTCTCCCTCACTAAACG
|
|
84
|
-
TAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGAGGTGGATTAA
|
|
85
|
-
ACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA
|
|
86
|
-
TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCC
|
|
87
|
-
TAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTAT
|
|
88
|
-
CTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCC
|
|
89
|
-
TAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATTCA
|
|
90
|
-
CAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCT
|
|
91
|
-
ACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAACG
|
|
92
|
-
TAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG
|
|
93
|
-
CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTA
|
|
94
|
-
GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT
|
|
95
|
-
AACAGCTAAGGACTGCAAAACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAA
|
|
96
|
-
TTAAGCTAAGCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCT
|
|
97
|
-
AAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAAAAAGGCGGGAG
|
|
98
|
-
AAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTC
|
|
99
|
-
GGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA
|
|
100
|
-
GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACA
|
|
101
|
-
AAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTC
|
|
102
|
-
TAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACA
|
|
103
|
-
TCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACCCA
|
|
104
|
-
TCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATATGG
|
|
105
|
-
CGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGC
|
|
106
|
-
TCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG
|
|
107
|
-
CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAG
|
|
108
|
-
CAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAAC
|
|
109
|
-
CCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAG
|
|
110
|
-
TCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACC
|
|
111
|
-
GCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAAC
|
|
112
|
-
ACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCAGGCTTCGGAA
|
|
113
|
-
TAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA
|
|
114
|
-
TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATAT
|
|
115
|
-
TTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCG
|
|
116
|
-
CTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGA
|
|
117
|
-
AATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGGCC
|
|
118
|
-
TGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGTACTACACGACACGTACTACG
|
|
119
|
-
TTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGGCT
|
|
120
|
-
TCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC
|
|
121
|
-
ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCC
|
|
122
|
-
TATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCC
|
|
123
|
-
TATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTT
|
|
124
|
-
GAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTGG
|
|
125
|
-
AGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAAAT
|
|
126
|
-
CTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGCC
|
|
127
|
-
TCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT
|
|
128
|
-
TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGC
|
|
129
|
-
TACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTT
|
|
130
|
-
CCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAA
|
|
131
|
-
TACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCAT
|
|
132
|
-
CCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGA
|
|
133
|
-
TCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCGA
|
|
134
|
-
CTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA
|
|
135
|
-
CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTAT
|
|
136
|
-
AATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAAC
|
|
137
|
-
AGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATA
|
|
138
|
-
CTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGA
|
|
139
|
-
ATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTACCCTATAGCACCCCCTCTA
|
|
140
|
-
CCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAG
|
|
141
|
-
AGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT
|
|
142
|
-
AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAA
|
|
143
|
-
CTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGA
|
|
144
|
-
ACCAAAATGAACGAAAATCTGTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCC
|
|
145
|
-
GCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATC
|
|
146
|
-
AACAACCGACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATA
|
|
147
|
-
ACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTTTT
|
|
148
|
-
ATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA
|
|
149
|
-
TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGC
|
|
150
|
-
TCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATC
|
|
151
|
-
CCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTA
|
|
152
|
-
CGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCACC
|
|
153
|
-
CTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCTA
|
|
154
|
-
CTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAGTA
|
|
155
|
-
AGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA
|
|
156
|
-
AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAG
|
|
157
|
-
CCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACAC
|
|
158
|
-
TAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACA
|
|
159
|
-
CACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTT
|
|
160
|
-
TTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAAT
|
|
161
|
-
TAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCC
|
|
162
|
-
TAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA
|
|
163
|
-
TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCT
|
|
164
|
-
ATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCA
|
|
165
|
-
TCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCT
|
|
166
|
-
CAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACATC
|
|
167
|
-
ACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATTTC
|
|
168
|
-
TGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGTACCGTTAACT
|
|
169
|
-
TCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA
|
|
170
|
-
TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCA
|
|
171
|
-
ACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCC
|
|
172
|
-
GCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAG
|
|
173
|
-
AAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAACAACTAACCTGCCACTAATAG
|
|
174
|
-
TTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACTAC
|
|
175
|
-
AAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACT
|
|
176
|
-
CATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG
|
|
177
|
-
CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTAC
|
|
178
|
-
TATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACA
|
|
179
|
-
CCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAG
|
|
180
|
-
CAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTAC
|
|
181
|
-
ATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACT
|
|
182
|
-
GACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACAGCCTAATTAT
|
|
183
|
-
TAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC
|
|
184
|
-
AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACC
|
|
185
|
-
CCTCACAATCATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACT
|
|
186
|
-
CTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGA
|
|
187
|
-
ACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATCAC
|
|
188
|
-
CCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACCCT
|
|
189
|
-
AGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCACT
|
|
190
|
-
AAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT
|
|
191
|
-
AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTT
|
|
192
|
-
ATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGT
|
|
193
|
-
ACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGAC
|
|
194
|
-
AAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGCTC
|
|
195
|
-
CATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACAT
|
|
196
|
-
AGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCAT
|
|
197
|
-
TCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA
|
|
198
|
-
CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACT
|
|
199
|
-
AATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAA
|
|
200
|
-
CCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCT
|
|
201
|
-
ACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAAC
|
|
202
|
-
ACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAA
|
|
203
|
-
CACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCAT
|
|
204
|
-
TACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA
|
|
205
|
-
CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCC
|
|
206
|
-
CATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAG
|
|
207
|
-
GCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACC
|
|
208
|
-
ACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAA
|
|
209
|
-
AAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTC
|
|
210
|
-
TTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGA
|
|
211
|
-
GCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA
|
|
212
|
-
TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATA
|
|
213
|
-
AACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATA
|
|
214
|
-
CTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGA
|
|
215
|
-
ATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCC
|
|
216
|
-
ATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA
|
|
217
|
-
TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATCCA
|
|
218
|
-
AGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT
|
|
219
|
-
CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCAC
|
|
220
|
-
TCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAA
|
|
221
|
-
AATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA
|
|
222
|
-
GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAAGT
|
|
223
|
-
CAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGCAC
|
|
224
|
-
ATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCAC
|
|
225
|
-
AACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC
|
|
226
|
-
ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT
|
|
227
|
-
TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCC
|
|
228
|
-
CTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTT
|
|
229
|
-
CTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACCCC
|
|
230
|
-
ACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATT
|
|
231
|
-
ACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC
|
|
232
|
-
ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC
|
|
233
|
-
AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTC
|
|
234
|
-
TACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTG
|
|
235
|
-
CCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAG
|
|
236
|
-
CACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTC
|
|
237
|
-
CTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCCCG
|
|
238
|
-
AGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACTAA
|
|
239
|
-
TCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA
|
|
240
|
-
CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCAC
|
|
241
|
-
CCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC
|
|
242
|
-
ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGC
|
|
243
|
-
TGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAACC
|
|
244
|
-
CATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATCAA
|
|
245
|
-
TACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAA
|
|
246
|
-
ACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC
|
|
247
|
-
CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACG
|
|
248
|
-
CAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATC
|
|
249
|
-
CAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAAT
|
|
250
|
-
CACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATC
|
|
251
|
-
AATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA
|
|
252
|
-
TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTACGG
|
|
253
|
-
ATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC
|
|
254
|
-
AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGT
|
|
255
|
-
AATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTG
|
|
256
|
-
AGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTT
|
|
257
|
-
GCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACGAAACGGGATC
|
|
258
|
-
AAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTACAC
|
|
259
|
-
AATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTATT
|
|
260
|
-
CTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC
|
|
261
|
-
TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC
|
|
262
|
-
TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCC
|
|
263
|
-
CATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTA
|
|
264
|
-
TTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGCTA
|
|
265
|
-
CCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCT
|
|
266
|
-
AATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTAT
|
|
267
|
-
AAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA
|
|
268
|
-
GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCT
|
|
269
|
-
CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACA
|
|
270
|
-
ACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAAT
|
|
271
|
-
ACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA
|
|
272
|
-
CAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCACC
|
|
273
|
-
CCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGC
|
|
274
|
-
CATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
|
|
275
|
-
TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCT
|
|
276
|
-
ACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT
|
|
277
|
-
CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGAC
|
|
278
|
-
ATCACGATG
|