better cfiles
This commit is contained in:
Celine Mercier
110
python/obitools3/commands/align.cfiles
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110
python/obitools3/commands/align.cfiles
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@ -0,0 +1,110 @@
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../../../src/obi_lcs.h
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../../../src/obi_lcs.c
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../../../src/obierrno.h
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../../../src/obierrno.c
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../../../src/upperband.h
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../../../src/upperband.c
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../../../src/sse_banded_LCS_alignment.h
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../../../src/sse_banded_LCS_alignment.c
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../../../src/obiblob.h
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../../../src/obiblob.c
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../../../src/utils.h
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../../../src/utils.c
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../../../src/obidms.h
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../../../src/obidms.c
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../../../src/libjson/json_utils.h
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../../../src/libjson/json_utils.c
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../../../src/libjson/cJSON.h
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../../../src/libjson/cJSON.c
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../../../src/obiavl.h
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../../../src/obiavl.c
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../../../src/bloom.h
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../../../src/bloom.c
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../../../src/crc64.h
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../../../src/crc64.c
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../../../src/murmurhash2.h
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../../../src/murmurhash2.c
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../../../src/obidmscolumn.h
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../../../src/obidmscolumn.c
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../../../src/obitypes.h
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../../../src/obitypes.c
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../../../src/obidmscolumndir.h
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../../../src/obidmscolumndir.c
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../../../src/obiblob_indexer.h
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../../../src/obiblob_indexer.c
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../../../src/obiview.h
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../../../src/obiview.c
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../../../src/hashtable.h
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../../../src/hashtable.c
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../../../src/linked_list.h
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../../../src/linked_list.c
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../../../src/obidmscolumn_array.h
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../../../src/obidmscolumn_array.c
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../../../src/obidmscolumn_blob.h
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../../../src/obidmscolumn_blob.c
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../../../src/obidmscolumn_idx.h
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../../../src/obidmscolumn_idx.c
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../../../src/obidmscolumn_bool.h
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../../../src/obidmscolumn_bool.c
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../../../src/obidmscolumn_char.h
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../../../src/obidmscolumn_char.c
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../../../src/obidmscolumn_float.h
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../../../src/obidmscolumn_float.c
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../../../src/obidmscolumn_int.h
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../../../src/obidmscolumn_int.c
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../../../src/obidmscolumn_qual.h
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../../../src/obidmscolumn_qual.c
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../../../src/obidmscolumn_seq.h
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../../../src/obidmscolumn_seq.c
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../../../src/obidmscolumn_str.h
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../../../src/obidmscolumn_str.c
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../../../src/array_indexer.h
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../../../src/array_indexer.c
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../../../src/char_str_indexer.h
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../../../src/char_str_indexer.c
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../../../src/dna_seq_indexer.h
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../../../src/dna_seq_indexer.c
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../../../src/encode.c
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../../../src/encode.h
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../../../src/uint8_indexer.c
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../../../src/uint8_indexer.h
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../../../src/build_reference_db.c
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../../../src/build_reference_db.h
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../../../src/kmer_similarity.c
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../../../src/kmer_similarity.h
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../../../src/obi_clean.c
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../../../src/obi_clean.h
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../../../src/obi_ecopcr.c
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../../../src/obi_ecopcr.h
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../../../src/obi_ecotag.c
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../../../src/obi_ecotag.h
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../../../src/obidms_taxonomy.c
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../../../src/obidms_taxonomy.h
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../../../src/obilittlebigman.c
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../../../src/obilittlebigman.h
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../../../src/_sse.h
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../../../src/obidebug.h
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../../../src/libecoPCR/libapat/CODES/dft_code.h
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../../../src/libecoPCR/libapat/CODES/dna_code.h
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../../../src/libecoPCR/libapat/CODES/prot_code.h
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../../../src/libecoPCR/libapat/apat_parse.c
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../../../src/libecoPCR/libapat/apat_search.c
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../../../src/libecoPCR/libapat/apat.h
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../../../src/libecoPCR/libapat/Gmach.h
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../../../src/libecoPCR/libapat/Gtypes.h
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../../../src/libecoPCR/libapat/libstki.c
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../../../src/libecoPCR/libapat/libstki.h
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../../../src/libecoPCR/libthermo/nnparams.h
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../../../src/libecoPCR/libthermo/nnparams.c
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../../../src/libecoPCR/ecoapat.c
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../../../src/libecoPCR/ecodna.c
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../../../src/libecoPCR/ecoError.c
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../../../src/libecoPCR/ecoMalloc.c
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../../../src/libecoPCR/ecoPCR.h
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@ -9,8 +9,8 @@ from obitools3.dms.view import RollbackException
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from obitools3.apps.config import logger
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from obitools3.utils cimport tobytes, str2bytes
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from obitools3.dms.capi.obialign cimport obi_lcs_align_one_column, \
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obi_lcs_align_two_columns
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from obitools3.dms.capi.obilcsalign cimport obi_lcs_align_one_column, \
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obi_lcs_align_two_columns
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import time
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import sys
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@ -27,14 +27,14 @@ def addOptions(parser):
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group=parser.add_argument_group('obi align specific options')
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group.add_argument('--input-2', '-I',
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action="store", dest="pouic:inputuri2",
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action="store", dest="align:inputuri2",
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metavar='<INPUT URI>',
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default="",
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type=str,
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help="Eventually, the URI of the second input to align with the first one.")
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group.add_argument('--threshold','-t',
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action="store", dest="pouic:threshold",
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action="store", dest="align:threshold",
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metavar='<THRESHOLD>',
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default=0.0,
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type=float,
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@ -48,41 +48,41 @@ def addOptions(parser):
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" (no threshold).")
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group.add_argument('--longest-length','-L',
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action="store_const", dest="pouic:reflength",
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action="store_const", dest="align:reflength",
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default=0,
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const=1,
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help="The reference length is the length of the longest sequence."
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" Default: the reference length is the length of the alignment.")
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group.add_argument('--shortest-length','-l',
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action="store_const", dest="pouic:reflength",
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action="store_const", dest="align:reflength",
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default=0,
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const=2,
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help="The reference length is the length of the shortest sequence."
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" Default: the reference length is the length of the alignment.")
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group.add_argument('--raw','-r',
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action="store_false", dest="pouic:normalize",
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action="store_false", dest="align:normalize",
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default=True,
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help="Raw score, not normalized. Default: score is normalized with the reference sequence length.")
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group.add_argument('--distance','-D',
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action="store_false", dest="pouic:similarity",
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action="store_false", dest="align:similarity",
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default=True,
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help="Score is expressed in distance. Default: score is expressed in similarity.")
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group.add_argument('--print-seq','-s',
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action="store_true", dest="pouic:printseq",
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action="store_true", dest="align:printseq",
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default=False,
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help="The nucleotide sequences are written in the output view. Default: they are not written.")
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group.add_argument('--print-count','-n',
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action="store_true", dest="pouic:printcount",
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action="store_true", dest="align:printcount",
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default=False,
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help="Sequence counts are written in the output view. Default: they are not written.")
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group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group
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action="store", dest="pouic:threadcount",
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action="store", dest="align:threadcount",
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metavar='<THREAD COUNT>',
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default=1,
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type=int,
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@ -168,8 +168,8 @@ def run(config):
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i_view_name_2 = b""
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i_column_name_2 = b""
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i_element_name_2 = b""
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if config['pouic']['inputuri2']:
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input_2 = open_uri(config['pouic']['inputuri2'],
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if config['align']['inputuri2']:
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input_2 = open_uri(config['align']['inputuri2'],
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dms_only=True)
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if input_2 is None:
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raise Exception("Could not read second input")
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@ -182,7 +182,7 @@ def run(config):
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if len(i_uri_2.split(b"/")) == 3:
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i_element_name_2 = i_uri_2.split(b"/")[2]
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if len(i_uri_2.split(b"/")) > 3:
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raise Exception("Input URI contains too many elements:", config['pouic']['inputuri2'])
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raise Exception("Input URI contains too many elements:", config['align']['inputuri2'])
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# If the 2 input DMS are not the same, temporarily import 2nd input view in first input DMS
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if i_dms != i_dms_2:
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@ -225,7 +225,7 @@ def run(config):
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i_view_list = [i_view_name]
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if original_i_view_name_2:
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i_view_list.append(original_i_view_name_2)
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comments = View.print_config(config, "pouic", command_line, input_dms_name=i_dms_list, input_view_name=i_view_list)
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comments = View.print_config(config, "align", command_line, input_dms_name=i_dms_list, input_view_name=i_view_list)
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# Call cython alignment function
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# Using default ID columns of the view. TODO discuss adding option
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@ -239,14 +239,14 @@ def run(config):
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input_elt_2_n = i_element_name_2, \
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id_column_1_n = b"", \
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id_column_2_n = b"", \
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threshold = config['pouic']['threshold'], \
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normalize = config['pouic']['normalize'], \
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reference = config['pouic']['reflength'], \
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similarity_mode = config['pouic']['similarity'], \
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print_seq = config['pouic']['printseq'], \
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print_count = config['pouic']['printcount'], \
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threshold = config['align']['threshold'], \
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normalize = config['align']['normalize'], \
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reference = config['align']['reflength'], \
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similarity_mode = config['align']['similarity'], \
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print_seq = config['align']['printseq'], \
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print_count = config['align']['printcount'], \
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comments = comments, \
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thread_count = config['pouic']['threadcount'])
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thread_count = config['align']['threadcount'])
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# If the input and output DMS are not the same, export result view to output DMS
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if i_dms != o_dms:
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110
python/obitools3/commands/alignpairedend.cfiles
Normal file
110
python/obitools3/commands/alignpairedend.cfiles
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../../../src/obi_lcs.h
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../../../src/obi_lcs.c
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../../../src/obierrno.h
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../../../src/obierrno.c
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../../../src/upperband.h
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../../../src/upperband.c
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../../../src/sse_banded_LCS_alignment.h
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../../../src/sse_banded_LCS_alignment.c
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../../../src/obiblob.h
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../../../src/obiblob.c
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../../../src/utils.h
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../../../src/utils.c
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../../../src/obidms.h
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../../../src/obidms.c
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../../../src/libjson/json_utils.h
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../../../src/libjson/json_utils.c
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../../../src/libjson/cJSON.h
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../../../src/libjson/cJSON.c
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../../../src/obiavl.h
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../../../src/obiavl.c
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../../../src/bloom.h
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../../../src/bloom.c
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../../../src/crc64.h
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../../../src/crc64.c
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../../../src/murmurhash2.h
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../../../src/murmurhash2.c
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../../../src/obidmscolumn.h
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../../../src/obidmscolumn.c
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../../../src/obitypes.h
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../../../src/obitypes.c
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../../../src/obidmscolumndir.h
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../../../src/obidmscolumndir.c
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../../../src/obiblob_indexer.h
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../../../src/obiblob_indexer.c
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../../../src/obiview.h
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../../../src/obiview.c
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../../../src/hashtable.h
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../../../src/hashtable.c
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../../../src/linked_list.h
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../../../src/linked_list.c
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../../../src/obidmscolumn_array.h
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../../../src/obidmscolumn_array.c
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../../../src/obidmscolumn_blob.h
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../../../src/obidmscolumn_blob.c
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../../../src/obidmscolumn_idx.h
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../../../src/obidmscolumn_idx.c
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../../../src/obidmscolumn_bool.h
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../../../src/obidmscolumn_bool.c
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../../../src/obidmscolumn_char.h
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../../../src/obidmscolumn_char.c
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../../../src/obidmscolumn_float.h
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../../../src/obidmscolumn_float.c
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../../../src/obidmscolumn_int.h
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../../../src/obidmscolumn_int.c
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../../../src/obidmscolumn_qual.h
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../../../src/obidmscolumn_qual.c
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../../../src/obidmscolumn_seq.h
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../../../src/obidmscolumn_seq.c
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../../../src/obidmscolumn_str.h
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../../../src/obidmscolumn_str.c
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../../../src/array_indexer.h
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../../../src/array_indexer.c
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../../../src/char_str_indexer.h
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../../../src/char_str_indexer.c
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../../../src/dna_seq_indexer.h
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../../../src/dna_seq_indexer.c
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../../../src/encode.c
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../../../src/encode.h
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../../../src/uint8_indexer.c
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../../../src/uint8_indexer.h
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../../../src/build_reference_db.c
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../../../src/build_reference_db.h
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../../../src/kmer_similarity.c
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../../../src/kmer_similarity.h
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../../../src/obi_clean.c
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../../../src/obi_clean.h
|
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../../../src/obi_ecopcr.c
|
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../../../src/obi_ecopcr.h
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../../../src/obi_ecotag.c
|
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../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
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../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
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|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/annotate.cfiles
Normal file
110
python/obitools3/commands/annotate.cfiles
Normal file
@ -0,0 +1,110 @@
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../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/build_ref_db.cfiles
Normal file
110
python/obitools3/commands/build_ref_db.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/clean.cfiles
Normal file
110
python/obitools3/commands/clean.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/count.cfiles
Normal file
110
python/obitools3/commands/count.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/ecopcr.cfiles
Normal file
110
python/obitools3/commands/ecopcr.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/ecotag.cfiles
Normal file
110
python/obitools3/commands/ecotag.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/export.cfiles
Normal file
110
python/obitools3/commands/export.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/grep.cfiles
Normal file
110
python/obitools3/commands/grep.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/head.cfiles
Normal file
110
python/obitools3/commands/head.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/history.cfiles
Normal file
110
python/obitools3/commands/history.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/import.cfiles
Normal file
110
python/obitools3/commands/import.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/less.cfiles
Normal file
110
python/obitools3/commands/less.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/ls.cfiles
Normal file
110
python/obitools3/commands/ls.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/ngsfilter.cfiles
Normal file
110
python/obitools3/commands/ngsfilter.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/sort.cfiles
Normal file
110
python/obitools3/commands/sort.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/stats.cfiles
Normal file
110
python/obitools3/commands/stats.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/tail.cfiles
Normal file
110
python/obitools3/commands/tail.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/test.cfiles
Normal file
110
python/obitools3/commands/test.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
110
python/obitools3/commands/uniq.cfiles
Normal file
110
python/obitools3/commands/uniq.cfiles
Normal file
@ -0,0 +1,110 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user