[Issue 9505] std.zlib seem to be bugged
https://issues.dlang.org/show_bug.cgi?id=9505 --- Comment #12 from github-bugzi...@puremagic.com --- Commits pushed to stable at https://github.com/dlang/phobos https://github.com/dlang/phobos/commit/5cf20bd8773e0f746c74b19137a03d699cdfe28b Fixed issues 3191 and 9505 https://github.com/dlang/phobos/commit/8e47bfc54c106b222835db3c3a37e81b52ab2f04 Merge pull request #5720 from kas-luthor/fix-zlib --
[Issue 9505] std.zlib seem to be bugged
https://issues.dlang.org/show_bug.cgi?id=9505 github-bugzi...@puremagic.com changed: What|Removed |Added Status|NEW |RESOLVED Resolution|--- |FIXED --
[Issue 9505] std.zlib seem to be bugged
https://issues.dlang.org/show_bug.cgi?id=9505 --- Comment #11 from github-bugzi...@puremagic.com --- Commits pushed to master at https://github.com/dlang/phobos https://github.com/dlang/phobos/commit/5cf20bd8773e0f746c74b19137a03d699cdfe28b Fixed issues 3191 and 9505 std.zlib.UnCompress.uncompress() now consumes as much of the input buffer as possible and extends / reallocates the output buffer accordingly It also sets inputEnded = 1 when Z_STREAM_END is returned from inflate() so that additional data after the compressed stream is not consumed https://github.com/dlang/phobos/commit/8e47bfc54c106b222835db3c3a37e81b52ab2f04 Merge pull request #5720 from kas-luthor/fix-zlib Fix zlib issues 3191, 9505 and 8779 merged-on-behalf-of: MetaLang --
[Issue 9505] std.zlib seem to be bugged
https://issues.dlang.org/show_bug.cgi?id=9505 Andre changed: What|Removed |Added CC||alver...@gmail.com --
[Issue 9505] std.zlib seem to be bugged
http://d.puremagic.com/issues/show_bug.cgi?id=9505 --- Comment #10 from bioinfornatics 2013-02-19 07:25:50 PST --- update uncompress function add zlibException any comments? -- Configure issuemail: http://d.puremagic.com/issues/userprefs.cgi?tab=email --- You are receiving this mail because: ---
[Issue 9505] std.zlib seem to be bugged
http://d.puremagic.com/issues/show_bug.cgi?id=9505 --- Comment #9 from bioinfornatics 2013-02-15 06:37:25 PST --- I updated the code http://dpaste.dzfl.pl/683c053b just add compress uncompress from the old code but fit with d2 way -- Configure issuemail: http://d.puremagic.com/issues/userprefs.cgi?tab=email --- You are receiving this mail because: ---
[Issue 9505] std.zlib seem to be bugged
http://d.puremagic.com/issues/show_bug.cgi?id=9505 --- Comment #8 from bioinfornatics 2013-02-14 09:49:19 PST --- (In reply to comment #7) > I guess that's because you are using winbits=15 instead of -15. BAM files > contain GZIP blocks with custom headers, so processing them is not so > straightforward. > > (I've developed a library for BAM files during last summer - > github.com/lomereiter/biod) > > (In reply to comment #0) > > Dear, > > when I try to read gzip compressed data with a byChunk modified to > > uncompress > > data at second loop uncompress raise an error: > > zlib.d(59): data error > > > > > > code: http://dpaste.1azy.net/0d8f6eac > > > > EXetoC show to me http://d.puremagic.com/issues/show_bug.cgi?id=3191 > > > > but this bug is really old is not possible to be this no ? > > > > $ ./zreader file.bam > > --> popFront() > > --> front() > > BAMP� > > --> popFront() > > --> front() Thanks a lot for your lib i will take a look. why not to create bioinformatic group for works together ? the problem show here is not about BGZF block i written a new module for zlib to fit with actual way to process in D as phobos range In anycase i think this code should replace the old one and give a review as zlib is D1 code -- Configure issuemail: http://d.puremagic.com/issues/userprefs.cgi?tab=email --- You are receiving this mail because: ---
[Issue 9505] std.zlib seem to be bugged
http://d.puremagic.com/issues/show_bug.cgi?id=9505 Artem Tarasov changed: What|Removed |Added CC||lomerei...@gmail.com --- Comment #7 from Artem Tarasov 2013-02-14 07:57:28 PST --- I guess that's because you are using winbits=15 instead of -15. BAM files contain GZIP blocks with custom headers, so processing them is not so straightforward. (I've developed a library for BAM files during last summer - github.com/lomereiter/biod) (In reply to comment #0) > Dear, > when I try to read gzip compressed data with a byChunk modified to uncompress > data at second loop uncompress raise an error: > zlib.d(59): data error > > > code: http://dpaste.1azy.net/0d8f6eac > > EXetoC show to me http://d.puremagic.com/issues/show_bug.cgi?id=3191 > > but this bug is really old is not possible to be this no ? > > $ ./zreader file.bam > --> popFront() > --> front() > BAMP� > --> popFront() > --> front() -- Configure issuemail: http://d.puremagic.com/issues/userprefs.cgi?tab=email --- You are receiving this mail because: ---
[Issue 9505] std.zlib seem to be bugged
http://d.puremagic.com/issues/show_bug.cgi?id=9505 --- Comment #6 from bioinfornatics 2013-02-14 03:36:31 PST --- I added some enhancement http://dpaste.dzfl.pl/683c053b -- Configure issuemail: http://d.puremagic.com/issues/userprefs.cgi?tab=email --- You are receiving this mail because: ---
[Issue 9505] std.zlib seem to be bugged
http://d.puremagic.com/issues/show_bug.cgi?id=9505 --- Comment #5 from bioinfornatics 2013-02-13 10:34:22 PST --- thanks for your much appropriated comment :-) I will try to enhance this. That was a snippet code to be able to read gz file in D as std.zlib and std.zip is unusable, unmaintened and in not in D philosophy ( use class instead struct, no phobos range and many bug ) -- Configure issuemail: http://d.puremagic.com/issues/userprefs.cgi?tab=email --- You are receiving this mail because: ---
[Issue 9505] std.zlib seem to be bugged
http://d.puremagic.com/issues/show_bug.cgi?id=9505 --- Comment #4 from monarchdo...@gmail.com 2013-02-13 09:41:39 PST --- Oh yeah, also, gzread will return -1 in case of an io error. you don't check for that. You'd probably want to use: _numberRead = gzread( _file, _buffer.ptr, cast(uint)_buffer.length ); errnoEnforce(numberRead >= 0); I can only guess a failed decompress sets an errno? Not sure. -- Configure issuemail: http://d.puremagic.com/issues/userprefs.cgi?tab=email --- You are receiving this mail because: ---
[Issue 9505] std.zlib seem to be bugged
http://d.puremagic.com/issues/show_bug.cgi?id=9505
monarchdo...@gmail.com changed:
What|Removed |Added
CC||monarchdo...@gmail.com
--- Comment #3 from monarchdo...@gmail.com 2013-02-13 09:25:07 PST ---
Both implementations have the fatal flaw of closing the file on first
destruction.
This makes passing a byZChunk (first case) or a (ZFile) second case a dangerous
operation.
Look into the "File" implementation, it should be reference counted, and only
close the file on the last actual destruction.
nitpick:
Once you've named your type ZFile, calling "byChunk" byZChunk is redudant. Just
leave it at byChunk:
auto r1 = File ("SRR077487_1.filt.fastq" ).byChunk();
auto r2 = ZFile("SRR077487_1.filt.fastq.gz").byChunk();
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[Issue 9505] std.zlib seem to be bugged
http://d.puremagic.com/issues/show_bug.cgi?id=9505 --- Comment #2 from bioinfornatics 2013-02-13 07:55:27 PST --- to fit more with std.stdio http://dpaste.dzfl.pl/683c053b I add a: - ZFile - rawRead method into ZFile - byZChunk use ZFile / ZFile.rawRead -- Configure issuemail: http://d.puremagic.com/issues/userprefs.cgi?tab=email --- You are receiving this mail because: ---
[Issue 9505] std.zlib seem to be bugged
http://d.puremagic.com/issues/show_bug.cgi?id=9505 --- Comment #1 from bioinfornatics 2013-02-13 07:15:41 PST --- i create a little code using etc.c.zlib to be able to use gzipped as a phobos range: http://dpaste.dzfl.pl/5b8db0a2 I would like your opinion on this code and if it could replace the old std.zlib.Uncompress if yes I could continue to work on to provides uncompress and compress way in D modern way you have the power -- Configure issuemail: http://d.puremagic.com/issues/userprefs.cgi?tab=email --- You are receiving this mail because: ---
