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ChangeLog
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2010-12-13 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Recognize `charstatelabels' as a valid
NEXUS command.
* lib/align/nexusil.l: Support tab characters just like plain
spaces in commands.
* lib/align/megal.l: Do correctly handle sequence names that start
with `mega' string.
* test/mega.sh: Exercize it.
2010-09-15 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embl*.[ly]: Relax accession number definition, to a
single word.
2010-09-06 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbank*.[ly]: Relax accession number definition,
by allowing a single word (that do not exceed allowed characters
per line). Problem reported by Marc Logghe.
* test/genbank.sh: New file to exercize GENBANK format.
2010-05-12 Nicolas Joly <njoly@pasteur.fr>
* src/format.c: Do reset entry number when counting entries during
format verification.
* test/count.sh: New test file, to exercize entries count.
2010-05-11 Nicolas Joly <njoly@pasteur.fr>
* src/squizz.c: Fix entries count which has been broken in
previous cleanup.
2010-05-10 Nicolas Joly <njoly@pasteur.fr>
* src/*.[ch]: Cleanup format handling, to not rely on implicit
structures copying between functions. No functional change.
2010-01-18 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Allow square brackets in sequence names
enclosed with quotes.
* test/nexus.sh: Exercise it.
2009-11-25 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Be more strict when checking for end tag in
ignored blocks, do only match complete word.
* test/nexus.sh: Exercise it.
2009-10-30 Nicolas Joly <njoly@pasteur.fr>
* lib/*/*.y: Switch from deprecated YYPARSE_PARAM define, to
`%parse-param' option.
2009-10-26 Nicolas Joly <njoly@pasteur.fr>
* lib/align/megay.y: Add support for long sequence names.
* test/mega.sh: Exercise it.
* lib/align/parse.c: Split `parse_seqadd()' function in 2 new ones
`parse_tmpupd()' which add the sequence name to a temporary buffer
and `parse_seqnew()' which really add the sequence.
* lib/align/*y.y: Adjust accordingly.
2009-10-22 Nicolas Joly <njoly@pasteur.fr>
* test/phylip[is].sh: Work around somw `grep -e' portability
problems.
* test/clustal.sh: Do not use `echo -n "msg"' which is not
portable, but `echo "msg" | tr -d "\n"' instead.
2009-10-09 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbanky.y: REFSEQ databank may have both DBLINK
and DBSOURCE keyword lines.
2009-09-17 Nicolas Joly <njoly@pasteur.fr>
* lib/align.c, lib/sequence.c: Do not redefine off_t, config.h
already handles it.
2009-09-07 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbankl.l: Update for new accessions found in
Refseq release 36.
2009-09-04 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embll.l: Do handle keywords that have an internal
`;' character.
* test/embl.sh: Exercise it.
* lib/sequence/sprotl.l: Do handle cross-reference data which
contain an internal `;' character.
* test/sprot.sh: New file to exercise SWISSPROT format.
* lib/sequence/genbankl.l: Work around a small header glitch
(extra leading space) in GenBank 173.0 release files.
2009-09-02 Nicolas Joly <njoly@pasteur.fr>
* lib/align/stockl.l: Sequence name may have a single character.
* test/stockholm.sh: Exercise it.
* lib/align/msfl.l: Increase allowed sequence names up to 80
characters.
* lib/align/megal.l: Do not choke on long Title lines.
2009-06-17 Nicolas Joly <njoly@pasteur.fr>
* lib/align/megal.l: Do ignore more comments.
* test/mega.sh: Exercise it.
2009-05-05 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustaly.y: Do handle/ignore base numbers which can
appear before the sequence chunk.
2009-04-23 Nicolas Joly <njoly@pasteur.fr>
* test/phylipi.sh: Add check for file with extra newlines at EOF.
2009-04-08 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Allow more than one command on a single
line.
2009-03-25 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbank*.[ly]: Add support for upcoming `DBLINK'
keyword in RefSeq.
2009-03-05 Nicolas Joly <njoly@pasteur.fr>
* lib/align/megal.l: Improve comment handling, by removing a
maximum size limit.
2009-03-02 Nicolas Joly <njoly@pasteur.fr>
* lib/align/megal.l: Ignore, for now, comment (enclosed with
quotes) after sequence name.
* test/mega.sh: Exercise it.
2009-02-18 Nicolas Joly <njoly@pasteur.fr>
* lib/align.c: Fix duplicate sequence names detection (the array
holding them was incorrectly sorted).
* test/align.sh: Exercise it.
* lib/align/megal.l: Increase allowed sequence name length from 40
to 50 characters.
2009-01-20 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/igl.l: Fix detection without newline at EOF.
* test/ig.sh: Exercise it.
* test/ig.sh: New file to exercise IG sequence format.
2009-01-09 Nicolas Joly <njoly@pasteur.fr>
* lib/align/phylipil.l: Correctly detect format without newline at
EOF, when sequences are on a single line.
* test/phylip[is].sh: Add checks for single line sequence, which
both PHYLIPI/PHYLIPS formats should match.
2008-12-12 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l, lib/align/nexusi.c: Add support for
sequence that contains spaces (must be enclosed with quotes).
* test/nexus.sh: Exercise it.
2008-10-16 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbankl.l: Do not choke on some UniProt secondary
accessions numbers (allow a mix of 6 alpha-numeric characters).
2008-10-07 Nicolas Joly <njoly@pasteur.fr>
* test/msf.sh: New file to exercise MSF alignment format.
* lib/align/megal.l: Ignore header line trailing spaces.
2008-09-30 Nicolas Joly <njoly@pasteur.fr>
* src/squizz.c, doc/alifmt.pod: Small typo fix.
* doc/alifmt.{man,html}: Regen.
2008-09-19 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Allow spaces before `begin' block keyword.
* lib/align/nexusil.l: Add `charlabels' command parsing.
* lib/align/stocky.y: Be robust against invalid sequence lines
(endless loop without space separator).
* test/stockholm.sh: New file, to exercise STOCKHOLM format.
2008-09-16 Nicolas Joly <njoly@pasteur.fr>
* lib/align/megal.l: Support identical `.' character in sequences.
* lib/align/mega.c: Replace all "identical" characters in
sequences.
* test/mega.sh: Exercise it.
2008-09-11 Nicolas Joly <njoly@pasteur.fr>
* lib/align/parse.c: Do not abort for unexpected sequence name in
alignment anymore.
* test/align.sh: Exercise it.
2008-09-10 Nicolas Joly <njoly@pasteur.fr>
* lib/align/phylip[is]*.[ly]: Handle correctly files without
newline at EOF (last sequence line).
* test/phylip[is].sh: Exercise them.
2008-09-08 Nicolas Joly <njoly@pasteur.fr>
* lib/align/megal.l: Handle correctly files without newline at
EOF (last sequence line).
* test/mega.sh: Exercise it.
2008-09-05 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/rawl.l: Allow gaps in RAW format (at least, to be
consistent with other sequence formats).
* test/raw.sh: Exercise it.
2008-09-02 Nicolas Joly <njoly@pasteur.fr>
* test/align.sh: New file for aligments generic checks.
* lib/sequence/utils.c: New file that holds sequence generic
utilities, such as a sequence name cleaner.
* lib/align/{mega,msf,nexusi}.c: Use it.
* lib/sequence/raw.c: Do not output gaps, just skip them for now.
* test/raw.sh: New file to exercise RAW format.
* test/align/fasta.seq: Updated.
* lib/sequence/embll.l: Fix EMBL parsing for anonymous entry.
* test/embl.sh: New file, to exercise it.
2008-09-01 Nicolas Joly <njoly@pasteur.fr>
* test/phylip[is].sh: Exercise sequence names with spaces.
* lib/align/phylip.[ch]: Simplify sequence names cleanup.
* lib/aligm/phylip[is].c: Adjust.
2008-08-29 Nicolas Joly <njoly@pasteur.fr>
* lib/align/stockl.l: Support tab characters just like spaces.
* lib/align/mega*.[ly]: Add support for old statement format.
* test/mega.sh: New file to exercise MEGA format.
* lib/align/clustall.l: Ignore empty lines without newline at EOF.
* test/clustal.sh: Exercise it.
2008-08-26 Nicolas Joly <njoly@pasteur.fr>
* lib/extern/text.c: Do not add more than a single space separator
when appending text buffers.
* lib/sequence/sprotl.l: Add support for new DE lines structure.
* lib/sequence/sprotl.l: Allow new `AGRICOLA' key in RX lines..
2008-07-28 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Add `*' as valid base character.
* lib/align/phylip[is]l.l: Do not allow empty line between header
and first sequence chunk.
* test/phylip[is].sh: New files, to exercise PHYLIPI/PHYLIPS
formats.
2008-07-25 Nicolas Joly <njoly@pasteur.fr>
* lib/align/stocky.y: Do not require empty line between header and
sequences.
* lib/align/nexusil.l: Ignore trailing spaces after MATRIX
keyword.
2008-05-21 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Adjust parsing to support missing newline
at EOF on sequence line.
* test/clustal.sh: Exercise it.
2008-04-24 Nicolas Joly <njoly@pasteur.fr>
* all: Remove unused DnaStrider sequence format.
2008-04-18 Nicolas Joly <njoly@pasteur.fr>
* doc/alifmt.pod: Add MEGA alignment sample.
* doc/alifmt.{man,html}: Regen.
2008-04-15 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Ignore trailing spaces after semi-column,
for matrix block end.
2008-04-03 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Now that spaces in token assignment are
globally supported, remove program specific hacks (ClustalW and
MacClade).
* lib/align/mega*: First try to support MEGA alignment format.
* lib/align.[ch], src/format.c: Adjust.
* test/align/mega.seq: New file in MEGA format.
* test/*ali.sh: Exercise it.
2008-03-19 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embll.l: Add `AGRICOLA' as a suppoprted resource
identifier for RX lines.
2008-03-11 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embll.l: Skip trailing spaces in accessions list
fields.
2008-03-07 Nicolas Joly <njoly@pasteur.fr>
* lib/align/stockl.l: Do not fail if last line, with end tag `//',
has no newline character.
* lib/align/nexusil.l: Handle command tokens which have spaces
around equal character (e.g `gap = -' instead of `gap=-').
* test/nexus.sh: New file, NEXUS format specific checks.
2008-03-06 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/fastal.l: Do not understand `.' as valid gap
character anymore, as most programs does not support it.
2008-02-28 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/nbrfl.l: Handle `D1' sequence type, for unknown
DNA, produced by EMBOSS programs.
* test/convali.sh: Remove `-s' flag in tests, now that its
behaviour has been changed to be the default.
2008-02-15 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/fasta.c: Do not output `?' as a valid gap
character.
2008-02-14 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustaly.y: Make empty line mandatory again between
header and first chunk of sequences.
* test/clustal.sh: Exercise it.
2008-02-13 Nicolas Joly <njoly@pasteur.fr>
* doc/*.html: Small update to add correct title.
2008-02-08 Nicolas Joly <njoly@pasteur.fr>
* lib/align.c: Speedup strict alignment check by removing nested
loops in duplicate names check.
* lib/align/fasta2.c: Fix invalid sequence buffer reallocation
size.
* src/squizz.c: Small update to make format verification (-f) work
with formats restrictions (-A/-S).
* doc/squizz.pod: Update documentation accordingly.
2008-02-06 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Do not fail if last consensus chunk does
not end with a newline (at EOF).
* test/clustal.sh: New file, for CLUSTAL format specific tests.
2008-02-05 Nicolas Joly <njoly@pasteur.fr>
* doc/*.pod: Do not output man(1) header/footer when generating
HTML documents. While here, remove generated index too.
2008-01-25 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/sprotl.l: Increase DR identifier value size to
match current UniProtKB limits.
2008-01-09 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustal*.[ly]: Improve format detection by adding a
terminator tag check.
2007-10-25 Nicolas Joly <njoly@pasteur.fr>
* src/format.c: Do not merge anymore PHYLIPI/PHYLIPS under generic
PHYLIP name (PHYLIP is still an alias for PHYLIPI).
* test/*ali.sh: Update tests accordingly.
* src/format.[ch]: Allow format display list to restricted to
sequence or alignment lists.
* src/squizz.c: Adjust accordingly.
2007-10-03 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embly.y: Add support for new ANN data class, which
has both CO and SQ sections.
2007-09-04 Nicolas Joly <njoly@pasteur.fr>
* src/squizz.c: Add a new flag `-n' to count and report detected
entries for a single type.
* src/format.[ch]: Count entries under strict format
detection/verification.
* doc/squizz.pod: Document it.
* test/squizz.sh: Check `-n' options conflicts.
2007-09-03 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbank*.[ly]: Add support for new `PRIMARY'
keyword in RefSeq databank.
2007-07-26 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/sprot*.[ly]: Add basic support for `Protein
Existence' (PE) lines.
2007-06-20 Nicolas Joly <njoly@pasteur.fr>
* src/squizz.c: Restrict intput to regular files.
* test/squizz.sh: Exercise it.
* lib/sequence/ig.c: Fix an infinite loop, when comments has an
unsplittable word of more than 78 characters.
2007-06-19 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embl*.[ly]: Add support for project (PR) lines.
2007-06-13 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embll.l: Allow lines with trailing spaces.
2007-06-11 Nicolas Joly <njoly@pasteur.fr>
* lib/align/stockl.l: Fix parsing, when comment line appears in
sequences block.
* lib/align/stock*.[ly]: Parsers cleanup, to make it more robust
to format variations.
* lib/align/msfl.l: Do not bail on expected empty lines that do
have some extra spaces.
2007-06-01 Nicolas Joly <njoly@pasteur.fr>
* doc/alifmt.pod: Add MSF sequence number limitation.
2007-04-04 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Do not validate NEXUS format for files
ending with invalid begin/end blocks other than characters or
data.
2007-03-08 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/gdel.l: Ignore all spaces characters in sequence
data.
2007-02-15 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/gdel.l: Ignore trailing spaces after sequence
names.
2007-02-14 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Allow structure and penality masks lines
in sequence chunks.
2007-02-13 Nicolas Joly <njoly@pasteur.fr>
* lib/align/parse.[ch]: Use return values for all parsing
functions, transmit errors to interrupt parsers.
* lib/align/*y.y: Adjust.
* src/squizz.c: Check for incompatible `-c' and `-s' options.
* test/squizz.sh: Exercise it.
2007-02-12 Nicolas Joly <njoly@pasteur.fr>
* src/squizz.c: Change `-s' default behaviour. Strict checks are
now enabled by default, and can be disabled with this option.
* doc/squizz.pod: Update accordingly.
2007-01-12 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusi*.[ly]: Sequence block separator can now be made
of multiple empty lines (even with comments in between).
2007-01-11 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embll.l: Skip EMBL internal fields, used in
sequence submisstion (e.g. `{ST,AC,BQ} * ').
2007-01-03 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/pirl.l: Do not break on large sequence lines, when
trying to detect empty lines (made by sreformat tool).
2006-12-11 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustal*.[ly]: Handle CLUSTAL files whitout empty line
between the header line and the first sequences block.
2006-12-04 Nicolas Joly <njoly@pasteur.fr>
* lib/align/phylipil.l: Ignore trailing spaces in header line.
* lib/align/phylipsl.l: Likewise.
2006-11-30 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence.c: Adjust sequence type detection to handle new `J'
(Leucine or IsoLeucine) and `O' (Pyrrolysine) amino acid codes.
2006-11-28 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Allow consensus lines without leading
spaces.
2006-11-14 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Ignore spaces characters in block end line.
* lib/align/phylipil.l: Ignore tabs, like spaces, in empty lines.
2006-10-27 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/sprot*.[ly]: Add support for OH (Organism Host)
lines.
2006-10-26 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbankl.l: Update genbank accession numbers for
WGS entries.
2006-10-25 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence.c: Add some debug messages in strict checking mode,
enabled by setting environment variable SQUIZZ_DEBUG.
2006-10-24 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusiy.y: Allow extra empty line before matrix block
end.
2006-10-23 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Allow `~' as gap character.
2006-10-21 Nicolas Joly <njoly@pasteur.fr>
* test/squizz.sh: Check for formats list.
2006-10-20 Nicolas Joly <njoly@pasteur.fr>
* doc/Makefile.am: Use `$(htmldir)' variable for HTML files
installation.
* lib/align/phylipsl.l: Do not allow empty line in sequence chunk.
2006-10-16 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbankl.l: Ignore TITLE fields from unknown
source, and empty lines before sequence.
* lib/sequence/embll.l: Allow `-' gap characters.
2006-10-13 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbanky.y: Make revision value `.<num>' optional
in VERSION field.
* lib/sequence/genbankl.l: Allow more than one space as separator
in VERSION field.
2006-10-12 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Ignore extra (empty) lines before MATRIX
block end.
2006-10-10 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbankl.l: Add `?' character as valid gap symbol.
2006-10-07 Nicolas Joly <njoly@pasteur.fr>
* lib/align/phylipil.l: Redo `Do not ignore extra numbers in
sequence' (from 2004-12-17), that crept in again ...
2006-10-05 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbanky.y: Allow single definition line without
ending character.
* lib/align/phylipsl.l: Ignore empty lines before each sequence
chunks.
* lib/align/clustall.l: Ignore empty/blank lines before the
CLUSTAL header tag.
2006-10-03 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/pirl.l: Add `-' as valid gap character.
* lib/align/nexusil.l: Ignore invalid `symbols = "..."' in NEXUS
MacClade generated files (should be <token>=<value>, without extra
spaces).
2006-10-02 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Revert previous, as it breaks detection
for files with last sequence newline but without consensus.
* lib/align/clustall.l: While here, simplify sequence blocks
separator by allowing more than a single newline.
2006-09-30 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Fix detection with missing newline (at
EOF) in last sequence line.
* lib/align/nexusil.l: Only parse sequence blocks (characters,
data), and ignore all other types (codons, paup, taxa, tree, ...).
2006-09-29 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/sprotl.l: Ignore more trailing spaces.
* lib/sequence/parse.c: Split `parse_dscadd()' into 2 functions.
One that prepend a separator space character if needed (for line
continuation), and one that do not (when text comes from the same
line).
* lib/sequence/*y.y: Adjust accordingly.
2006-09-28 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Allow another tag version, with first
character uppercase (eg. Clustal).
* lib/sequence/genbank.c: Fix infinite loop with unsplittable long
words (without `-' character) in DEFINITION field output.
* lib/sequence/embl.c: Likewise.
2006-09-26 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Allow lowercase version of `CLUSTAL' tag
in header.
2006-09-25 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbanky.y: Update RefSeq format detection to use
`DBSOURCE' (protein) or `PROJECT' (genomic) lines, but not both.
* lib/sequence/genbankl.l: Ignore extra `REGION:' datas in
`ACCESSION' line.
2006-09-21 Nicolas Joly <njoly@pasteur.fr>
* doc/Makefile.am: Remove leading space in format samples for HTML
generated files.
* lib/sequence/striderl.l: Allow `.' as valid gap character.
2006-09-16 Nicolas Joly <njoly@pasteur.fr>
* lib/align/phylip.c: Add missing "error.h" include.
2006-09-09 Nicolas Joly <njoly@pasteur.fr>
* lib/*/*l.l: Add `nounput' option to fix some lint warnings about
unused `unput()' function.
2006-09-08 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Ignore trailing spaces following a comment
block.
2006-09-04 Nicolas Joly <njoly@pasteur.fr>
* lib/align/phylip.[ch]: New file for PHYLIP common functions,
shared by both interleaved and sequential formats.
* lib/align/phylip[is].c: Use common code to fix sequence names
with invalid characters.
2006-09-01 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustal.c: Check that at least one sequence name is
larger than 15 characters (do not always check all names).
* src/format.c: Turn warnings into errors for conversion problems.
2006-08-30 Nicolas Joly <njoly@pasteur.fr>
* test/sequence/*.seq: Update all available databanks entries from
GenBank, GenPept, RefSeq and UniProtKB.
* lib/sequence/genbank.c: Use localtime_r() instead of
localtime() like other formats.
2006-08-29 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Allow `*' character (stop codon) in protein
alignments.
2006-08-28 Nicolas Joly <njoly@pasteur.fr>
* lib/align/msfl.l: Allow '?' as a valid gap character.
* lib/align/msf.c: Adjust.
2006-08-24 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Ignore trailing tabs too, just like
spaces.
2006-06-22 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embl*.[ly]: Add support for contig entries.
* lib/sequence/embl.c: Update ID line output to the new EMBL
format (rel. 87 - june 2006).
* test/sequence/embl.seq: Refresh sample entry from databank.
* lib/align/nexusil.l: Ignore invalid `gap= -' construct in NEXUS
format made by ClustalW program (spaces are illegal as gap
characters).
2006-06-16 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embll.l: Do not allow `;' character in sequence
names anymore, to preprare ID line format change in EMBL.
* lib/sequence/genbankl.l: Update header detection for GenPept
daily update files.
2006-06-15 Nicolas Joly <njoly@pasteur.fr>
* lib/align.c: Add some debug messages in strict checking mode,
enabled by setting environment variable SQUIZZ_DEBUG.
2006-06-09 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Support `?' as valid gap character.
* lib/align/clustal.c: Adjust accordingly.
2006-06-06 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/pirl.l: Small updates to support files generated by
Sean Eddy sreformat tool (mostly spacing fixes ...).
2006-05-19 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Fix empty lines detection (to be ignored).
2006-05-17 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embl*.[ly]: Simplify ID lines parsing.
2006-05-08 Nicolas Joly <njoly@pasteur.fr>
* lib/align.c: Do no abort on alignment allocation problem, return
NULL; like sequence already do.
* align.[ch]: Do alignment initialisation during allocation, and
remove specific function.
* sequence.[ch]: Likewise.
2006-05-07 Nicolas Joly <njoly@pasteur.fr>
* lib/align/parse.c: Fix a small memory leak, when parsing
sequence names which already exists.
* lib/align.c: Fix two others in alignment object cleanup.
2006-05-05 Nicolas Joly <njoly@pasteur.fr>
* lib/align/stock*.*: New files for STOCKHOLM alignment format
(from Sean Eddy HMMER package).
* lib/align.[ch], src/format.c: Adjust accordingly.
* test/align/stock.seq: New STOCKHOLM sample file.
* test/fmtali.sh, test/convali.sh: Exercise it.
* doc/squizz.pod, doc/alifmt.pod: Update documentation.
2006-04-27 Nicolas Joly <njoly@pasteur.fr>
* lib/align/msfl.l: Do not assume that `Name:' is followed by at
least a space character.
2006-04-24 Nicolas Joly <njoly@pasteur.fr>
* lib/align/msfy.y: Make empty line optional for first sequence
block (remains mandatory for others).
2006-04-19 Nicolas Joly <njoly@pasteur.fr>
* test/squizz.sh: Exercise recently added options.
2006-04-18 Nicolas Joly <njoly@pasteur.fr>
* src/squizz.c: Add `-A' and `-S' options to restrict detection to
alignments or sequence formats.
* src/format.[ch]: Adjust accordingly.
* doc/squizz.pod: Document them.
2006-04-14 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Ignore lines with spaces only during
sequences block parsing.
2006-04-05 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbankl.l: Added `protein id' format to supported
accession list (found on NCBI protein entries).
2006-04-03 Nicolas Joly <njoly@pasteur.fr>
* src/format.c: Allow strict checks with format verification too,
not only for detection.
* doc/squizz.pod: Document `strict checks' operations.
2006-03-31 Nicolas Joly <njoly@pasteur.fr>
* doc/alifmt.pod: Small formatting adjustements to not exceed 80
characters line limit.
* doc/seqfmt.pod: Likewise.
2006-03-16 Nicolas Joly <njoly@pasteur.fr>
* lib/align/parse.c: Fix a stupid buffer mistake, which arise when
trying to add a new sequence name without leading spaces.
* lib/align/msf*.[ly]: Make the position numbers (before each
sequence block) optional.
* src/format.c: Simplify format detection code, no functional
change.
2006-03-14 Nicolas Joly <njoly@pasteur.fr>
* lib/align/msf.c: Small updates in MSF format output to match
reality: add an extra space after the sequence, remove leading `0'
characters to the checksum, and fix names alignment in header.
* lib/align/msf.c: Right justify names in sequence lines.
2006-03-13 Nicolas Joly <njoly@pasteur.fr>
* test/squizz.sh: New test file, to check for base operations
(options, ...).
2006-03-10 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Do not allow new command if previous one is
unfinished. Strengthen command line continuation.
2006-03-09 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustaly.y: Allow longer description text in CLUSTAL
header line.
2006-03-08 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbankl.l: Adjust GenPept VERSION field, which use
the entry name where other databanks use accession number.
* lib/sequence/genbank*.[ly]: Add support for new `PROJECT'
field in REFSEQ databank; and make `DBSOURCE' field optional.
2006-03-07 Nicolas Joly <njoly@pasteur.fr>
* lib/align.c, lib/sequence.c: Add `#include <sys/types.h>' for
off_t definition on Darwin.
* src/format.c: Likewise.
* lib/sequence/sprot*.[ly]: Add support for old RX lines format.
2006-02-02 Nicolas Joly <njoly@pasteur.fr>
* src/squizz.c: Add `-f' option, to check for only one format
instead of trying to detect it.
2006-01-05 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embll.l: Fix sequence detection for entries with
more than 10Mb.
* lib/sequence/embl*.[ly]: Add support for `Third Party
Annotation' AH and AS lines.
2006-01-02 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/genbankl.l: Update Accession Number definitions.
* lib/sequence/genbank[yl].*: Add minimal support for CONTIG
entries.
* lib/sequence.[ch]: Add some strict sequence checking code.
* src/format.c: Use it to reject entries without sequence.
2006-01-02 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/*y.y: Remove unneeded check for empty sequence
string.
2005-10-25 Nicolas Joly <njoly@pasteur.fr>
* lib/align.c: Sequence names, in strict alignment checks, must
now be unique.
* test/align/fasta.seq: Adjust.
2005-10-13 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embly.y: CC lines can be empty.
2005-07-11 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/nbrfl.l: Allow `?' as a valid gap character.
* lib/align/msfl.l: Increase sequence names up to 55 characters.
2005-07-06 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/embll.l: OC nodes can be split across lines.
* lib/sequence/embly.y: Adjust.
* lib/sequence/embly.y: Organism classification list can be empty.
2005-07-01 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/nbrfl.l: Allow `~' as a valid gap character.
2005-06-27 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Allow token values enclosed with quotes,
because it contains spaces.
* lib/align/nexusiy.y: Adjust.
2005-06-24 Nicolas Joly <njoly@pasteur.fr>
* lib/align/clustall.l: Consensus lines may begin with tabs.
2005-06-20 Nicolas Joly <njoly@pasteur.fr>
* lib/align/nexusil.l: Allow multi-line comment.
2005-06-14 Nicolas Joly <njoly@pasteur.fr>
* lib/align.c: Remove all occurences of `strlen(x->str)', and use
already precalculated `x->strlen' instead.
* lib/align/msf.c: Likewise.
2005-06-06 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/sprot.c: Fix output for sequence names with more
than 10 characters.
* lib/sequence/sprotl.l: Fix Swissprot OC nodes detection to allow
non-terminal `.' character.
2005-05-29 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/sproty.y: Make all organism fields optional.
* lib/sequence/sproty.y: Allow quaternary identifier for database
cross-references.
2005-05-27 Nicolas Joly <njoly@pasteur.fr>
* lib/sequence/rawy.y: Fix incorrect format detection (multiple
raw sequences in the same file).
2005-05-26 Nicolas Joly <njoly@pasteur.fr>