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parallel: Fail if -a file is not seekable for --pipepart.

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Ole Tange 2015-05-15 22:05:48 +02:00
parent fd5622b2c6
commit 456f63d2bc
2 changed files with 10 additions and 3 deletions
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9
doc/release_new_version
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@ -230,12 +230,11 @@ New in this release:
taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/ (check it) taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/ (check it)
* <<har ikke svaret og accepteret ansvar>> GNU Parallel was used in: Large Scale Author Name Disambiguation in Digital Libraries http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7004487&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7004487 * <<Afventer updateret publisering>> GNU Parallel was used in: Large Scale Author Name Disambiguation in Digital Libraries http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7004487&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7004487
* << Update forventet juni >> GNU Parallel was used in: SISRS: Site Identification from Short Read Sequences https://github.com/rachelss/SISRS/ * << Update forventet juni >> GNU Parallel was used in: SISRS: Site Identification from Short Read Sequences https://github.com/rachelss/SISRS/
* <<kontaktet 2015-05-06>> GNU Parallel was used (unfortunately with wrong citation) in: TADSim: Discrete Event-Based Performance Prediction for Temperature-Accelerated Dynamics http://vruehle.de/publications/2015c.pdf * <<kontaktet 2015-05-09>> GNU Parallel was used (unfortunately with wrong citation) in: TADSim: Discrete Event-Based Performance Prediction for Temperature-Accelerated Dynamics http://vruehle.de/publications/2015c.pdf
* GNU Parallel was cited in: CIDER: a pipeline for detecting waves of coordinated transcriptional regulation in gene expression time-course data http://biorxiv.org/content/biorxiv/early/2015/03/17/012518.full.pdf * GNU Parallel was cited in: CIDER: a pipeline for detecting waves of coordinated transcriptional regulation in gene expression time-course data http://biorxiv.org/content/biorxiv/early/2015/03/17/012518.full.pdf
@ -261,6 +260,10 @@ taxator-tk http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/ (check it)
* Run multiple ssh commands in parallel with GNU Parallel http://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html * Run multiple ssh commands in parallel with GNU Parallel http://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html
* Importing huge databases faster https://www.lullabot.com/blog/article/importing-huge-databases-faster
* Run multiple ssh commands in parallel with GNU Parallel https://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html/comment-page-1
* Parallel? Gnu parallel! https://debian.pro/1834 * Parallel? Gnu parallel! https://debian.pro/1834
* Bug fixes and man page updates. * Bug fixes and man page updates.

4
src/parallel
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@ -184,6 +184,10 @@ sub pipe_part_files {
# @commands that will cat_partial each part # @commands that will cat_partial each part
my ($file) = @_; my ($file) = @_;
my $buf = ""; my $buf = "";
if(not -f $file) {
::error("$file is not a seekable file.");
::wait_and_exit(255);
}
my $header = find_header(\$buf,open_or_exit($file)); my $header = find_header(\$buf,open_or_exit($file));
# find positions # find positions
my @pos = find_split_positions($file,$opt::blocksize,length $header); my @pos = find_split_positions($file,$opt::blocksize,length $header);