From 9ccddd5280de219ed57b1fb90b6db51dba5aeb64 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Tue, 19 Feb 2019 14:11:29 +0100 Subject: [PATCH] better cfiles --- python/obitools3/commands/align.cfiles | 110 ++++++++++++++++++ .../commands/{pouic.pxd => align.pxd} | 0 .../commands/{pouic.pyx => align.pyx} | 44 +++---- .../obitools3/commands/alignpairedend.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/annotate.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/build_ref_db.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/clean.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/count.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/ecopcr.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/ecotag.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/export.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/grep.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/head.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/history.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/import.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/less.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/ls.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/ngsfilter.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/sort.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/stats.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/tail.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/test.cfiles | 110 ++++++++++++++++++ python/obitools3/commands/uniq.cfiles | 110 ++++++++++++++++++ 23 files changed, 2332 insertions(+), 22 deletions(-) create mode 100644 python/obitools3/commands/align.cfiles rename python/obitools3/commands/{pouic.pxd => align.pxd} (100%) rename python/obitools3/commands/{pouic.pyx => align.pyx} (88%) create mode 100644 python/obitools3/commands/alignpairedend.cfiles create mode 100644 python/obitools3/commands/annotate.cfiles create mode 100644 python/obitools3/commands/build_ref_db.cfiles create mode 100644 python/obitools3/commands/clean.cfiles create mode 100644 python/obitools3/commands/count.cfiles create mode 100644 python/obitools3/commands/ecopcr.cfiles create mode 100644 python/obitools3/commands/ecotag.cfiles create mode 100644 python/obitools3/commands/export.cfiles create mode 100644 python/obitools3/commands/grep.cfiles create mode 100644 python/obitools3/commands/head.cfiles create mode 100644 python/obitools3/commands/history.cfiles create mode 100644 python/obitools3/commands/import.cfiles create mode 100644 python/obitools3/commands/less.cfiles create mode 100644 python/obitools3/commands/ls.cfiles create mode 100644 python/obitools3/commands/ngsfilter.cfiles create mode 100644 python/obitools3/commands/sort.cfiles create mode 100644 python/obitools3/commands/stats.cfiles create mode 100644 python/obitools3/commands/tail.cfiles create mode 100644 python/obitools3/commands/test.cfiles create mode 100644 python/obitools3/commands/uniq.cfiles diff --git a/python/obitools3/commands/align.cfiles b/python/obitools3/commands/align.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/align.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/pouic.pxd b/python/obitools3/commands/align.pxd similarity index 100% rename from python/obitools3/commands/pouic.pxd rename to python/obitools3/commands/align.pxd diff --git a/python/obitools3/commands/pouic.pyx b/python/obitools3/commands/align.pyx similarity index 88% rename from python/obitools3/commands/pouic.pyx rename to python/obitools3/commands/align.pyx index 2f5eb6a..d465ece 100644 --- a/python/obitools3/commands/pouic.pyx +++ b/python/obitools3/commands/align.pyx @@ -9,8 +9,8 @@ from obitools3.dms.view import RollbackException from obitools3.apps.config import logger from obitools3.utils cimport tobytes, str2bytes -from obitools3.dms.capi.obialign cimport obi_lcs_align_one_column, \ - obi_lcs_align_two_columns +from obitools3.dms.capi.obilcsalign cimport obi_lcs_align_one_column, \ + obi_lcs_align_two_columns import time import sys @@ -27,14 +27,14 @@ def addOptions(parser): group=parser.add_argument_group('obi align specific options') group.add_argument('--input-2', '-I', - action="store", dest="pouic:inputuri2", + action="store", dest="align:inputuri2", metavar='', default="", type=str, help="Eventually, the URI of the second input to align with the first one.") group.add_argument('--threshold','-t', - action="store", dest="pouic:threshold", + action="store", dest="align:threshold", metavar='', default=0.0, type=float, @@ -48,41 +48,41 @@ def addOptions(parser): " (no threshold).") group.add_argument('--longest-length','-L', - action="store_const", dest="pouic:reflength", + action="store_const", dest="align:reflength", default=0, const=1, help="The reference length is the length of the longest sequence." " Default: the reference length is the length of the alignment.") group.add_argument('--shortest-length','-l', - action="store_const", dest="pouic:reflength", + action="store_const", dest="align:reflength", default=0, const=2, help="The reference length is the length of the shortest sequence." " Default: the reference length is the length of the alignment.") group.add_argument('--raw','-r', - action="store_false", dest="pouic:normalize", + action="store_false", dest="align:normalize", default=True, help="Raw score, not normalized. Default: score is normalized with the reference sequence length.") group.add_argument('--distance','-D', - action="store_false", dest="pouic:similarity", + action="store_false", dest="align:similarity", default=True, help="Score is expressed in distance. Default: score is expressed in similarity.") group.add_argument('--print-seq','-s', - action="store_true", dest="pouic:printseq", + action="store_true", dest="align:printseq", default=False, help="The nucleotide sequences are written in the output view. Default: they are not written.") group.add_argument('--print-count','-n', - action="store_true", dest="pouic:printcount", + action="store_true", dest="align:printcount", default=False, help="Sequence counts are written in the output view. Default: they are not written.") group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group - action="store", dest="pouic:threadcount", + action="store", dest="align:threadcount", metavar='', default=1, type=int, @@ -168,8 +168,8 @@ def run(config): i_view_name_2 = b"" i_column_name_2 = b"" i_element_name_2 = b"" - if config['pouic']['inputuri2']: - input_2 = open_uri(config['pouic']['inputuri2'], + if config['align']['inputuri2']: + input_2 = open_uri(config['align']['inputuri2'], dms_only=True) if input_2 is None: raise Exception("Could not read second input") @@ -182,7 +182,7 @@ def run(config): if len(i_uri_2.split(b"/")) == 3: i_element_name_2 = i_uri_2.split(b"/")[2] if len(i_uri_2.split(b"/")) > 3: - raise Exception("Input URI contains too many elements:", config['pouic']['inputuri2']) + raise Exception("Input URI contains too many elements:", config['align']['inputuri2']) # If the 2 input DMS are not the same, temporarily import 2nd input view in first input DMS if i_dms != i_dms_2: @@ -225,7 +225,7 @@ def run(config): i_view_list = [i_view_name] if original_i_view_name_2: i_view_list.append(original_i_view_name_2) - comments = View.print_config(config, "pouic", command_line, input_dms_name=i_dms_list, input_view_name=i_view_list) + comments = View.print_config(config, "align", command_line, input_dms_name=i_dms_list, input_view_name=i_view_list) # Call cython alignment function # Using default ID columns of the view. TODO discuss adding option @@ -239,14 +239,14 @@ def run(config): input_elt_2_n = i_element_name_2, \ id_column_1_n = b"", \ id_column_2_n = b"", \ - threshold = config['pouic']['threshold'], \ - normalize = config['pouic']['normalize'], \ - reference = config['pouic']['reflength'], \ - similarity_mode = config['pouic']['similarity'], \ - print_seq = config['pouic']['printseq'], \ - print_count = config['pouic']['printcount'], \ + threshold = config['align']['threshold'], \ + normalize = config['align']['normalize'], \ + reference = config['align']['reflength'], \ + similarity_mode = config['align']['similarity'], \ + print_seq = config['align']['printseq'], \ + print_count = config['align']['printcount'], \ comments = comments, \ - thread_count = config['pouic']['threadcount']) + thread_count = config['align']['threadcount']) # If the input and output DMS are not the same, export result view to output DMS if i_dms != o_dms: diff --git a/python/obitools3/commands/alignpairedend.cfiles b/python/obitools3/commands/alignpairedend.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/alignpairedend.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/annotate.cfiles b/python/obitools3/commands/annotate.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/annotate.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/build_ref_db.cfiles b/python/obitools3/commands/build_ref_db.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/build_ref_db.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/clean.cfiles b/python/obitools3/commands/clean.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/clean.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/count.cfiles b/python/obitools3/commands/count.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/count.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/ecopcr.cfiles b/python/obitools3/commands/ecopcr.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/ecopcr.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/ecotag.cfiles b/python/obitools3/commands/ecotag.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/ecotag.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/export.cfiles b/python/obitools3/commands/export.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/export.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/grep.cfiles b/python/obitools3/commands/grep.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/grep.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/head.cfiles b/python/obitools3/commands/head.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/head.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/history.cfiles b/python/obitools3/commands/history.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/history.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/import.cfiles b/python/obitools3/commands/import.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/import.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/less.cfiles b/python/obitools3/commands/less.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/less.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/ls.cfiles b/python/obitools3/commands/ls.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/ls.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/ngsfilter.cfiles b/python/obitools3/commands/ngsfilter.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/ngsfilter.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/sort.cfiles b/python/obitools3/commands/sort.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/sort.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/stats.cfiles b/python/obitools3/commands/stats.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/stats.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/tail.cfiles b/python/obitools3/commands/tail.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/tail.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/test.cfiles b/python/obitools3/commands/test.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/test.cfiles @@ -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 + + + + + + + diff --git a/python/obitools3/commands/uniq.cfiles b/python/obitools3/commands/uniq.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/commands/uniq.cfiles @@ -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 + + + + + + +