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Diffstat (limited to 'sci-biology/meme/files/meme-4.11.2_p2-patch1.patch')
| -rw-r--r-- | sci-biology/meme/files/meme-4.11.2_p2-patch1.patch | 383 |
1 files changed, 0 insertions, 383 deletions
diff --git a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch b/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch deleted file mode 100644 index 30a182f8f43a..000000000000 --- a/sci-biology/meme/files/meme-4.11.2_p2-patch1.patch +++ /dev/null @@ -1,383 +0,0 @@ ---- a/doc/alphabet-format.html -+++ b/doc/alphabet-format.html -@@ -233,7 +233,7 @@ - providing a reference on the meaning of the symbols used. If present, the - symbol name must be the second field.</p> - <p>The "<span class="pdat">name</span>" follows the rules of -- <a href="qstr">quoted text</a>.</p> -+ <a href="#qstr">quoted text</a>.</p> - </div> - <h5>color</h5> - <div class="indent"> ---- a/doc/release-notes.html -+++ b/doc/release-notes.html -@@ -14,8 +14,26 @@ - <h2>Motif-based sequence analysis tools</h2> - </div> - <h2>MEME Suite Release Notes</h2> -+ <hr> -+ <b>MEME version 4.11.2 patch 1 -- June 16, 2016</b> -+ <ul> -+ <li> -+ <b>Bug fixes</b> -+ <ul> -+ <li> -+ Fixed bug in MCAST 4.11.2 that caused it to prematurely truncate -+ reading the sequence file. -+ </li> -+ <li> -+ Modified MEME to fall back to a simple Dirichlet prior when -+ using DNA or a custom alphabet with a prior that requires -+ a prior library, but no prior libray is specified. -+ </li> -+ </ul -+ </li> -+ </ul> -+ <p> - <hr> -- <p> - <b>MEME version 4.11.2 -- May 5 2016</b> - </p> - <ul> ---- a/src/fasta-io.c -+++ b/src/fasta-io.c -@@ -14,6 +14,7 @@ - #include "alphabet.h" - #include "fasta-io.h" - #include "io.h" -+#include "seq-reader-from-fasta.h" - #include "prior-reader-from-psp.h" - #include "seq.h" - -@@ -159,61 +160,6 @@ - } - - /**************************************************************************** -- * Read raw sequence until a new sequence is encountered or too many letters -- * are read. The new sequence is appended to the end of the given -- * sequence. -- * -- * Return: Was the sequence read completely? -- ****************************************************************************/ --static BOOLEAN_T read_raw_sequence_from_reader( -- DATA_BLOCK_READER_T *fasta_reader, // Sequence source -- char* name, // Sequence ID (used in error messages). -- ALPH_T* alph, // Alphabet in use -- unsigned int offset, // Current position in raw_sequence. -- unsigned int max_chars, // Maximum chars in raw_sequence. -- char* raw_sequence // Pre-allocated sequence. --) { -- // tlb; change a_char to integer so it will compile on SGI -- int a_char; -- int start_update; -- BOOLEAN_T return_value = TRUE; -- -- // Start at the end of the given sequence. -- assert(offset < max_chars); -- -- DATA_BLOCK_T *seq_block = new_sequence_block(max_chars - offset); -- return_value = !fasta_reader->get_next_block(fasta_reader, seq_block); -- -- char *seq_buffer = get_sequence_from_data_block(seq_block); -- size_t seq_buffer_size = get_num_read_into_data_block(seq_block); -- int i; -- for (i = 0; i < seq_buffer_size; ++i) { -- a_char = seq_buffer[i]; -- // Skip non-alphabetic characters. -- if (!isalnum(a_char) && a_char != '-' && a_char != '*' && a_char != '.') { -- if ((a_char != ' ') && (a_char != '\t') && (a_char != '\n') && (a_char != '\r')) { -- fprintf(stderr, "Warning: Skipping character %c in sequence %s.\n", -- a_char, name); -- } -- } else { -- // skip check if unknown alph -- if (alph != NULL && !alph_is_known(alph, a_char)) { -- fprintf(stderr, "Warning: Converting illegal character %c to %c ", -- a_char, alph_wildcard(alph)); -- fprintf(stderr, "in sequence %s.\n", name); -- a_char = alph_wildcard(alph); -- } -- raw_sequence[offset] = (char) a_char; -- ++offset; -- } -- } -- -- raw_sequence[offset] = '\0'; -- free_data_block(seq_block); -- return(return_value); --} -- --/**************************************************************************** - * Read one sequence from a file in Fasta format. - * - * Return: Was a sequence successfully read? -@@ -320,44 +266,6 @@ - } - - /**************************************************************************** -- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -- * and copy them in to the raw sequence in the SEQ_T object starting at the -- * given buffer offset. -- ****************************************************************************/ --void read_one_fasta_segment_from_reader( -- DATA_BLOCK_READER_T *fasta_reader, -- size_t max_size, -- size_t buffer_offset, -- SEQ_T *sequence --) { -- -- assert(sequence != NULL); -- assert(get_seq_length(sequence) <= max_size); -- -- // Get the raw sequence buffer from the SEQ_T -- char *raw_sequence = get_raw_sequence(sequence); -- if (raw_sequence == NULL) { -- // Allocate space for raw sequence if not done yet. -- raw_sequence = mm_malloc(sizeof(char) * max_size + 1); -- raw_sequence[0] = 0; -- } -- -- // Read a block of sequence charaters into the -- // raw sequence buffer for the SEQ_T. -- char *name = get_seq_name(sequence); -- BOOLEAN_T is_complete = read_raw_sequence_from_reader( -- fasta_reader, -- name, -- NULL, //FIXME this is dodgy, need a proper way of getting the alphabet. The fasta_reader has it but it is not accessable! -- buffer_offset, -- max_size, -- raw_sequence -- ); -- set_raw_sequence(raw_sequence, is_complete, sequence); -- --} -- --/**************************************************************************** - * Read all the sequences from a FASTA file at once. - Multiple files can be appended by calling this more than once. - ****************************************************************************/ ---- a/src/fasta-io.h -+++ b/src/fasta-io.h -@@ -43,19 +43,6 @@ - ); - - /**************************************************************************** -- * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -- * and copy them in to the raw sequence in the SEQ_T object starting at the -- * given buffer offset. -- ****************************************************************************/ --void read_one_fasta_segment_from_reader( -- DATA_BLOCK_READER_T *fasta_reader, -- size_t max_size, -- size_t buffer_offset, -- SEQ_T* sequence --); -- -- --/**************************************************************************** - * Read all the sequences from a file in Fasta format. - ****************************************************************************/ - void read_many_fastas ---- a/src/init.c -+++ b/src/init.c -@@ -767,10 +767,16 @@ - if (alph_is_builtin_protein(alph)) { // default mixture prior for proteins - plib_name = make_path_to_file(get_meme_etc_dir(), PROTEIN_PLIB); - } else { -- fprintf(stderr, "The prior library must be specified for DNA or custom " -- "alphabets when specifiying a prior type of 'dmix', 'mega' " -- "or 'megap'."); -- exit(1); -+ fprintf( -+ stderr, -+ "WARNING: When using DNA or a custom alphabet, " -+ "and specifiying a prior type of\n" -+ "'dmix', 'mega' or 'megap', a prior library must be provided.\n" -+ "No prior library was provided, so a simple Dirichlet prior will be used.\n" -+ ); -+ prior = "dirichlet"; -+ ptype = Dirichlet; -+ if (beta <= 0) beta = 0.01; // default b = 0.01 for simple Dirichlet - } - } - } ---- a/src/seq-reader-from-fasta.c -+++ b/src/seq-reader-from-fasta.c -@@ -639,11 +639,140 @@ - return fasta_reader->current_position; - } - -+ -+/**************************************************************************** -+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -+ * and copy them in to the raw sequence in the SEQ_T object starting at the -+ * given buffer offset. -+ ****************************************************************************/ -+void read_one_fasta_segment_from_reader( -+ DATA_BLOCK_READER_T *fasta_reader, -+ size_t max_size, -+ size_t offset, -+ SEQ_T *sequence -+) { -+ -+ -+ assert(sequence != NULL); -+ assert(offset < max_size); -+ -+ // Get the raw sequence buffer from the SEQ_T -+ char *raw_sequence = get_raw_sequence(sequence); -+ if (raw_sequence == NULL) { -+ // Allocate space for raw sequence if not done yet. -+ raw_sequence = mm_malloc(sizeof(char) * max_size + 1); -+ raw_sequence[0] = 0; -+ } -+ -+ // Read a block of sequence charaters into the -+ // raw sequence buffer for the SEQ_T, starting at offset. -+ BOOLEAN_T is_complete = read_raw_sequence_from_reader( -+ fasta_reader, -+ max_size - offset, -+ raw_sequence + offset -+ ); -+ set_raw_sequence(raw_sequence, is_complete, sequence); -+} -+ -+/**************************************************************************** -+ * Read raw sequence until a new sequence is encountered or too many letters -+ * are read. -+ * -+ * Return: Was the sequence read completely? -+ ****************************************************************************/ -+BOOLEAN_T read_raw_sequence_from_reader( -+ DATA_BLOCK_READER_T *reader, // Sequence source -+ unsigned int max_chars, // Maximum chars in raw_sequence. -+ char* raw_sequence // Pre-allocated sequence buffer. -+) { -+ -+ SEQ_READER_FROM_FASTA_T *fasta_reader -+ = (SEQ_READER_FROM_FASTA_T *) get_data_block_reader_data(reader); -+ -+ // Read sequence into temp. buffer from the sequence file. -+ char buffer[max_chars]; -+ long start_file_pos = ftell(fasta_reader->fasta_file); -+ size_t seq_index = 0; -+ size_t total_read = 0; -+ while (seq_index < max_chars) { -+ -+ size_t num_char_read = fread( -+ buffer, -+ sizeof(char), -+ max_chars - seq_index, -+ fasta_reader->fasta_file -+ ); -+ fasta_reader->current_position += num_char_read; -+ total_read += num_char_read; -+ -+ if (feof(fasta_reader->fasta_file)) { -+ fasta_reader->at_end_of_file = TRUE; -+ } -+ else if (num_char_read < (max_chars - seq_index)) { -+ die( -+ "Error while reading sequence from file:%s.\nError message: %s\n", -+ fasta_reader->filename, -+ strerror(ferror(fasta_reader->fasta_file)) -+ ); -+ } -+ -+ size_t i; -+ for(i = 0; i < num_char_read; ++i) { -+ char c = buffer[i]; -+ assert(c != 0); -+ if (isspace(c)) { -+ // Skip over white space -+ fasta_reader->at_start_of_line = (c == '\n'); -+ } -+ else if (c == '>' && fasta_reader->at_start_of_line == TRUE) { -+ // We found the start of a new sequence while trying -+ // to fill the buffer. Leave the buffer incomplete. -+ // and wind back the file -+ fseek(fasta_reader->fasta_file, start_file_pos + i - 1, SEEK_SET); -+ fasta_reader->current_position = start_file_pos + i - 1; -+ fasta_reader->at_end_of_seq = TRUE; -+ fasta_reader->at_start_of_line = FALSE; -+ fasta_reader->at_end_of_file = FALSE; -+ break; -+ } -+ else { -+ fasta_reader->at_start_of_line = FALSE; -+ // Check that character is legal in alphabet. -+ // If not, replace with wild card character. -+ if (alph_is_known(fasta_reader->alphabet, c)) { -+ raw_sequence[seq_index] = c; -+ } -+ else { -+ raw_sequence[seq_index] = alph_wildcard(fasta_reader->alphabet); -+ fprintf( -+ stderr, -+ "Warning: %c is not a valid character in %s alphabet.\n" -+ " Converting %c to %c.\n", -+ c, -+ alph_name(fasta_reader->alphabet), -+ c, -+ raw_sequence[i] -+ ); -+ } -+ ++seq_index; -+ } -+ } -+ if (fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file) { -+ break; -+ } -+ } -+ -+ raw_sequence[seq_index] = '\0'; -+ return(fasta_reader->at_end_of_seq | fasta_reader->at_end_of_file); -+} -+ - /****************************************************************************** -- * Fills in the next data block for the sequence. -- * During the first call for the sequence it fills in the full data block. -- * On successive calls, shifts the sequence in the block down one position -- * and reads one more character. -+ * Populates the data block for the with the next block of sequence. -+ * -+ * During the first call for the sequence it fills in a buffer from a file, -+ * The sequence pointer in the data block is set to point at the start of the buffer. -+ * On successive calls, the sequence pointer in the block is shifted down one position -+ * in the buffer. When the end of the buffer is reached, it is filled again from the file. - * - * Returns TRUE if it was able to completely fill the block, FALSE if - * the next sequence or EOF was reached before the block was filled. ---- a/src/seq-reader-from-fasta.h -+++ b/src/seq-reader-from-fasta.h -@@ -37,5 +37,30 @@ - int * end_ptr // end position of sequence (chr:\d+-(\d+)) - ); - -+/**************************************************************************** -+ * Read raw sequence until a new sequence is encountered or too many letters -+ * are read. -+ * -+ * Return: Was the sequence read completely? -+ ****************************************************************************/ -+BOOLEAN_T read_raw_sequence_from_reader( -+ DATA_BLOCK_READER_T *fasta_reader, // Sequence source -+ unsigned int max_chars, // Maximum chars in raw_sequence. -+ char* raw_sequence // Pre-allocated sequence. -+); -+ -+/**************************************************************************** -+ * Read up to max_chars letters of one sequence from a DATA_BLOCK_T readder -+ * and copy them in to the raw sequence in the SEQ_T object starting at the -+ * given buffer offset. -+ ****************************************************************************/ -+void read_one_fasta_segment_from_reader( -+ DATA_BLOCK_READER_T *reader, -+ size_t max_size, -+ size_t offset, -+ SEQ_T *sequence -+); -+ -+ - size_t get_current_pos_from_seq_reader_from_fasta(DATA_BLOCK_READER_T *reader); - #endif |