ensembl-gh-mirror issueshttps://gitlab.ebi.ac.uk/groups/ensembl-gh-mirror/-/issues2020-03-26T00:00:04Zhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/91Log Wording Ambiguous2020-03-26T00:00:04ZMarek SzubaLog Wording Ambiguous*Created by: DarioS*
I get an error such as
```
Configuring Bio-DB-HTS-3.01 ... N/A
! Configure failed for Bio-DB-HTS-3.01. See /users/stgrad/dario/.cpanm/work/1585179865.8235/build.log for details.
```
I use `cpanm` to install...*Created by: DarioS*
I get an error such as
```
Configuring Bio-DB-HTS-3.01 ... N/A
! Configure failed for Bio-DB-HTS-3.01. See /users/stgrad/dario/.cpanm/work/1585179865.8235/build.log for details.
```
I use `cpanm` to install it. When I look at the log file it's not clear what the error is
```
Running Build.PL
This module requires HTSlib (http://htslib.org/)
Install it if you have not done so already.
This script will attempt to locate HTSlib by looking for htslib/hts.h
and libhts.a / libhts.so in:
1. --htslib command line argument
2. HTSLIB_DIR environment variable
3. --prefix command line argument (which also sets installation location)
4. Alien::HTSlib dependency resolver
5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
6. common library locations: /usr /usr/local, /usr/share, /opt/local
-> N/A
-> FAIL Configure failed for Bio-DB-HTS-3.01. See /users/stgrad/dario/.cpanm/work/1585179865.8235/build.log for details.
```
"This script will attempt to locate HTSlib ..." doesn't explain whether the script successfully found HTSlib or not for my particular instance. Also, the end of the log file advises "See /users/stgrad/dario/.cpanm/work/1585179865.8235/build.log for details." But, I am already viewing that file, so the user should not be instructed to re-open the log file they already opened.
I'm baffled why this script can't detect HTSlib on the server I'm using:
```
~$ dpkg --list | grep hts
ii libhts-dev:amd64 1.9-11 amd64 development files for the HTSlib
ii libhts2:amd64 1.9-11 amd64 C library for high-throughput sequencing data formats
ii python-htseq 0.11.2-1 amd64 Python high-throughput genome sequencing read analysis utilities
```https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/89Request to honour POSIX ACLs2019-11-14T23:28:54ZMarek SzubaRequest to honour POSIX ACLs*Created by: CanWood*
Hi folks.
Would it be possible to have the access checks on bam files enhanced to check whether or not POSIX ACLs will allow users to access files? [HTS.pm line 1387](https://github.com/Ensembl/Bio-DB-HTS/blob/...*Created by: CanWood*
Hi folks.
Would it be possible to have the access checks on bam files enhanced to check whether or not POSIX ACLs will allow users to access files? [HTS.pm line 1387](https://github.com/Ensembl/Bio-DB-HTS/blob/master/lib/Bio/DB/HTS.pm#L1387) uses filetest access and, according to the [perldoc for filetest](https://perldoc.perl.org/filetest.html)
> ...you may encounter surprises if your program runs on a system that uses ACLs, since the stat() information won't reflect the actual permissions.
Any chance these tests could be enhanced to allow use of ACL on supporting systems?
Thanks!https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/79lzma.h file missing on Mac OSx High Sierra v.10.13.6 2018-09-26T08:28:38ZMarek Szubalzma.h file missing on Mac OSx High Sierra v.10.13.6 *Created by: SabriJamal*
Hi,
I was installing Bio-DB-HTS package and run into an issue with the lzma.h header file. I apparently have the LZMA library installed but don't have the lzma.h header file. I installed the XZ library in ord...*Created by: SabriJamal*
Hi,
I was installing Bio-DB-HTS package and run into an issue with the lzma.h header file. I apparently have the LZMA library installed but don't have the lzma.h header file. I installed the XZ library in order to get the lzma.h header file although then it got saved in...
/usr/local/Cellar/xz/5.2.4/include/lzma.h
I got around this by adding the following in bold to a line in the INSTALL.pl file
-e '/usr/include/lzma.h' **|| '/usr/local/Cellar/xz/5.2.4/include/lzma.h'** or die <<END;
I made a post in stackoverflow regarding issues installing Bio:Perl where another user mentioned that on his Mac OSx High Sierra he had the lzma.h file located in **/usr/local/include** and not as required, **/usr/include** (see post below)
https://stackoverflow.com/questions/52468476/issues-installing-perl-module-bioperl?noredirect=1#comment91917414_52468476
I have seen quite a few post with similar issue but concerning different problems, all relating to the missing lzma.h header file.
Kind regards
Sabrihttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/40padded_alignment() produces invalid output2018-09-04T17:44:30ZMarek Szubapadded_alignment() produces invalid output*Created by: AlexanderDilthey*
Hi,
The padded_alignment() function sometimes produces invalid output, in that the strings that specify the pairwise alignment are not of equal length.
Interestingly, this only happens (on the same a...*Created by: AlexanderDilthey*
Hi,
The padded_alignment() function sometimes produces invalid output, in that the strings that specify the pairwise alignment are not of equal length.
Interestingly, this only happens (on the same alignment) when using CRAM format -- BAM and SAM are fine.
I also get these warnings:
substr outside of string at /home/diltheyat/perl5/lib/perl5/x86_64-linux-thread-multi/Bio/DB/HTS/AlignWrapper.pm line 307.
Use of uninitialized value in concatenation (.) or string at /home/diltheyat/perl5/lib/perl5/x86_64-linux-thread-multi/Bio/DB/HTS/AlignWrapper.pm line 307.
Files to reproduce this error:
Reference genome GRCh38_full_plus_hs38d1_analysis_set_minus_alts.fa: https://gembox.cbcb.umd.edu/shared/graph_hackathon/reference/GRCh38_full_plus_hs38d1_analysis_set_minus_alts.fa
CRAM/SAM with one test alignment: https://www.dropbox.com/s/2dbb413ulfrhpma/testCase.zip?dl=0
Code:
use strict;
use warnings;
use Data::Dumper;
use Bio::DB::HTS;
my $referenceFasta = 'GRCh38_full_plus_hs38d1_analysis_set_minus_alts.fa';
my $sam = Bio::DB::HTS->new(-fasta => $referenceFasta, -bam => 'testCase.cram');
my $alignment_iterator = $sam->features(-iterator => 1);
while(my $alignment = $alignment_iterator->next_seq)
{
my ($ref,$matches,$query) = $alignment->padded_alignment;
unless(length($ref) == length($query))
{
warn Dumper("Alignment length mismatch", length($ref), length($query), $alignment->query->name);
next;
}
}
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/65Ensure header single point of access via PP API2018-03-16T15:11:05ZMarek SzubaEnsure header single point of access via PP API*Created by: avullo*
Se discussions #62 *Created by: avullo*
Se discussions #62 https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/56Calling coverage on a BAM re-fetches the header every time2018-03-14T16:13:04ZMarek SzubaCalling coverage on a BAM re-fetches the header every time*Created by: ah19*
A possible performance issue rather than a bug:
https://github.com/Ensembl/Bio-DB-HTS/blob/master/lib/Bio/DB/HTS.pm#L1951
```perl
...
my $header = $self->{hts_file}->header_read;
my ( $id, $s, $e ) = $h...*Created by: ah19*
A possible performance issue rather than a bug:
https://github.com/Ensembl/Bio-DB-HTS/blob/master/lib/Bio/DB/HTS.pm#L1951
```perl
...
my $header = $self->{hts_file}->header_read;
my ( $id, $s, $e ) = $header->parse_region($region);
return unless defined $id;
# parse_region may return a very high value if no end specified
$end = $e >= 1 << 29 ? $header->target_len->[$id] : $e;
...
```
Calling `$self->header` uses the cached versionhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/XML-To-Blockly/-/issues/10Unattachable block2016-09-20T14:22:47ZMarek SzubaUnattachable block*Created by: anujk14*
The problem occurs if a ref contains a magic node, and it is called in the following way:
1) First it is called from a non-magic parent like <element>
2) Then, it is called by a magic parent, i.e., a <oneOrMore>/<c...*Created by: anujk14*
The problem occurs if a ref contains a magic node, and it is called in the following way:
1) First it is called from a non-magic parent like <element>
2) Then, it is called by a magic parent, i.e., a <oneOrMore>/<choice> etc.
If we reverse the order, the problem goes away.
Example to check the bug: bug_07_unattachable_block_for_oneOrMore_ref.rng