diff --git a/python/obitools3/apps/arguments.cfiles b/python/obitools3/apps/arguments.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/apps/arguments.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/apps/command.cfiles b/python/obitools3/apps/command.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/apps/command.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/apps/config.cfiles b/python/obitools3/apps/config.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/apps/config.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/apps/logging.cfiles b/python/obitools3/apps/logging.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/apps/logging.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/apps/progress.cfiles b/python/obitools3/apps/progress.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/apps/progress.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/apps/temp.cfiles b/python/obitools3/apps/temp.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/apps/temp.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/dms/column/column.cfiles b/python/obitools3/dms/column/column.cfiles new file mode 100644 index 0000000..19f702c --- /dev/null +++ b/python/obitools3/dms/column/column.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/dms/column/column_idx.cfiles b/python/obitools3/dms/column/column_idx.cfiles new file mode 100644 index 0000000..19f702c --- /dev/null +++ b/python/obitools3/dms/column/column_idx.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/dms/column/typed_column/bool.cfiles b/python/obitools3/dms/column/typed_column/bool.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/bool.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/dms/column/typed_column/char.cfiles b/python/obitools3/dms/column/typed_column/char.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/char.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/dms/column/typed_column/float.cfiles b/python/obitools3/dms/column/typed_column/float.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/float.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/dms/column/typed_column/int.cfiles b/python/obitools3/dms/column/typed_column/int.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/int.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/dms/column/typed_column/qual.cfiles b/python/obitools3/dms/column/typed_column/qual.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/qual.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/dms/column/typed_column/seq.cfiles b/python/obitools3/dms/column/typed_column/seq.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/seq.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/dms/column/typed_column/str.cfiles b/python/obitools3/dms/column/typed_column/str.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/column/typed_column/str.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/dms/dms.cfiles b/python/obitools3/dms/dms.cfiles index 9425abb..fcf4279 100755 --- a/python/obitools3/dms/dms.cfiles +++ b/python/obitools3/dms/dms.cfiles @@ -1,50 +1,110 @@ -../../../src/array_indexer.c +../../../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/build_reference_db.c -../../../src/char_str_indexer.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/hashtable.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/linked_list.c -../../../src/murmurhash2.c -../../../src/obi_lcs.c +../../../src/kmer_similarity.h ../../../src/obi_clean.c +../../../src/obi_clean.h ../../../src/obi_ecopcr.c -../../../src/libecoPCR/libthermo/nnparams.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/libjson/cJSON.c -../../../src/libjson/json_utils.c -../../../src/obiavl.c -../../../src/obiblob_indexer.c -../../../src/obiblob.c -../../../src/obidms_taxonomy.c -../../../src/obidms.c -../../../src/obidmscolumn_array.c -../../../src/obidmscolumn_blob.c -../../../src/obidmscolumn_bool.c -../../../src/obidmscolumn_char.c -../../../src/obidmscolumn_float.c -../../../src/obidmscolumn_idx.c -../../../src/obidmscolumn_int.c -../../../src/obidmscolumn_qual.c -../../../src/obidmscolumn_seq.c -../../../src/obidmscolumn_str.c -../../../src/obidmscolumn.c -../../../src/obidmscolumndir.c -../../../src/obi_ecotag.c -../../../src/obierrno.c -../../../src/obilittlebigman.c -../../../src/obitypes.c -../../../src/obiview.c -../../../src/sse_banded_LCS_alignment.c -../../../src/uint8_indexer.c -../../../src/upperband.c -../../../src/utils.c +../../../src/libecoPCR/ecoPCR.h + + + + + + + diff --git a/python/obitools3/dms/obiseq.cfiles b/python/obitools3/dms/obiseq.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/dms/obiseq.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/dms/object.cfiles b/python/obitools3/dms/object.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/dms/object.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/dms/taxo/taxo.cfiles b/python/obitools3/dms/taxo/taxo.cfiles new file mode 100644 index 0000000..19f702c --- /dev/null +++ b/python/obitools3/dms/taxo/taxo.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/dms/view/typed_view/view_NUC_SEQS.cfiles b/python/obitools3/dms/view/typed_view/view_NUC_SEQS.cfiles new file mode 100644 index 0000000..72668a9 --- /dev/null +++ b/python/obitools3/dms/view/typed_view/view_NUC_SEQS.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/dms/view/view.cfiles b/python/obitools3/dms/view/view.cfiles new file mode 100644 index 0000000..19f702c --- /dev/null +++ b/python/obitools3/dms/view/view.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/files/linebuffer.cfiles b/python/obitools3/files/linebuffer.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/files/linebuffer.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/files/uncompress.cfiles b/python/obitools3/files/uncompress.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/files/uncompress.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/files/universalopener.cfiles b/python/obitools3/files/universalopener.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/files/universalopener.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/format/fasta.cfiles b/python/obitools3/format/fasta.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/format/fasta.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/format/fastq.cfiles b/python/obitools3/format/fastq.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/format/fastq.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/format/header.cfiles b/python/obitools3/format/header.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/format/header.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/libalign/_assemble.cfiles b/python/obitools3/libalign/_assemble.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/_assemble.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/libalign/_dynamic.cfiles b/python/obitools3/libalign/_dynamic.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/_dynamic.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/libalign/_freeendgap.cfiles b/python/obitools3/libalign/_freeendgap.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/_freeendgap.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/libalign/_freeendgapfm.cfiles b/python/obitools3/libalign/_freeendgapfm.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/_freeendgapfm.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/libalign/_nws.cfiles b/python/obitools3/libalign/_nws.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/_nws.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/libalign/_qsassemble.cfiles b/python/obitools3/libalign/_qsassemble.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/_qsassemble.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/libalign/_qsrassemble.cfiles b/python/obitools3/libalign/_qsrassemble.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/_qsrassemble.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/libalign/_rassemble.cfiles b/python/obitools3/libalign/_rassemble.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/_rassemble.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/libalign/_solexapairend.cfiles b/python/obitools3/libalign/_solexapairend.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/_solexapairend.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/libalign/apat_pattern.cfiles b/python/obitools3/libalign/apat_pattern.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/apat_pattern.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/libalign/shifted_ali.cfiles b/python/obitools3/libalign/shifted_ali.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/libalign/shifted_ali.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/parsers/embl.cfiles b/python/obitools3/parsers/embl.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/parsers/embl.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/parsers/embl_genbank_features.cfiles b/python/obitools3/parsers/embl_genbank_features.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/parsers/embl_genbank_features.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/parsers/fasta.cfiles b/python/obitools3/parsers/fasta.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/parsers/fasta.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/parsers/fastq.cfiles b/python/obitools3/parsers/fastq.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/parsers/fastq.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/parsers/header.cfiles b/python/obitools3/parsers/header.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/parsers/header.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/parsers/ngsfilter.cfiles b/python/obitools3/parsers/ngsfilter.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/parsers/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/parsers/tab.cfiles b/python/obitools3/parsers/tab.cfiles new file mode 100755 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/parsers/tab.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/parsers/universal.cfiles b/python/obitools3/parsers/universal.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/parsers/universal.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/uri/decode.cfiles b/python/obitools3/uri/decode.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/uri/decode.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/utils.cfiles b/python/obitools3/utils.cfiles index d7ee383..73ce179 100755 --- a/python/obitools3/utils.cfiles +++ b/python/obitools3/utils.cfiles @@ -1,50 +1,110 @@ -../../src/array_indexer.c +../../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/build_reference_db.c -../../src/char_str_indexer.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/hashtable.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/linked_list.c -../../src/murmurhash2.c -../../src/obi_lcs.c +../../src/kmer_similarity.h ../../src/obi_clean.c +../../src/obi_clean.h ../../src/obi_ecopcr.c -../../src/libecoPCR/libthermo/nnparams.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/libjson/cJSON.c -../../src/libjson/json_utils.c -../../src/obiavl.c -../../src/obiblob_indexer.c -../../src/obiblob.c -../../src/obidms_taxonomy.c -../../src/obidms.c -../../src/obidmscolumn_blob.c -../../src/obidmscolumn_bool.c -../../src/obidmscolumn_char.c -../../src/obidmscolumn_float.c -../../src/obidmscolumn_idx.c -../../src/obidmscolumn_int.c -../../src/obidmscolumn_qual.c -../../src/obidmscolumn_seq.c -../../src/obidmscolumn_str.c -../../src/obidmscolumn_array.c -../../src/obidmscolumn.c -../../src/obidmscolumndir.c -../../src/obi_ecotag.c -../../src/obierrno.c -../../src/obilittlebigman.c -../../src/obitypes.c -../../src/obiview.c -../../src/sse_banded_LCS_alignment.c -../../src/uint8_indexer.c -../../src/upperband.c -../../src/utils.c +../../src/libecoPCR/ecoPCR.h + + + + + + + diff --git a/python/obitools3/writers/fasta.cfiles b/python/obitools3/writers/fasta.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/writers/fasta.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/writers/fastq.cfiles b/python/obitools3/writers/fastq.cfiles new file mode 100644 index 0000000..fcf4279 --- /dev/null +++ b/python/obitools3/writers/fastq.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 + + + + + + +