ensembl-gh-mirror issueshttps://gitlab.ebi.ac.uk/groups/ensembl-gh-mirror/-/issues2017-01-28T12:03:35Zhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/39BufferOverflow error2017-01-28T12:03:35ZMarek SzubaBufferOverflow error*Created by: Schmurf87*
Hi,
I have a code which is trying to retrieve each 2690 phase 3 samples.cram from 1000 genomes ftp to get their coverage (and analyse it before going to the next sample).
Here is the function which have the ...*Created by: Schmurf87*
Hi,
I have a code which is trying to retrieve each 2690 phase 3 samples.cram from 1000 genomes ftp to get their coverage (and analyse it before going to the next sample).
Here is the function which have the purpose to retrieve coverage for a given sample and chromosome:
```perl
sub loadingSampleCov {
my $chr = shift;
my $sample = shift;
my $sam = Bio::DB::HTS->new(-bam => 'ftp://ftp.1000genomes.ebi.ac.uk/vol1/'.$sample->adresse,
);
my $coverage = \$sam->get_features_by_location(-type=>'coverage',-seq_id=>$chr);
#return $coverage;
}
```
For example, the "$sample->adresse" could be equal to "ftp/data_collections/1000_genomes_project/data/CEU/NA12828/alignment/NA12828.alt_bwamem_GRCh38DH.20150718.CEU.low_coverage.cram".
The code I ran simply loop on each sample and call the above function, like that:
```perl
my $progress = Term::ProgressBar->new(scalar(@samples));
my $c = 0;
for my $sample(@samples){
$c++;
print "$c: sample ".$sample->id."\n";
loadingSampleCov($chr, $sample);
$progress->update($_);
print ".. Done ! \n";
}
```
Unfortunatly, when arrives the 339 sample, the script throws the following [error](https://gist.github.com/Schmurf87/9e5b89fdf0ceebb48291e2d8305c8cff).
I tried to remove the 339 sample (NA11840) from the list of sample but the script still throws the same error at the new 339 sample.
I ran this code on a 16GB computer, and the max ram (see the end of the error message, under the Maximum resident set size (kbytes) line) is 5.5GB, which is not limitant.
Maybe there is a way to empty the buffer after each sample, in order to avoid this error...
Thank you in advance for your help.
https://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/29Build failure under Fedora 232016-08-04T10:51:20ZMarek SzubaBuild failure under Fedora 23*Created by: biogberg*
Build fails under Fedora 23 (4.3.3-303.fc23.x86_64). Perl is 5.22.1 (system), gcc is 5.3.1 (system).
`perl Build.PL`
runs cleanly.
Output from
`perl Build build`
is shown at the end. Compilation dies on:
`cc1: e...*Created by: biogberg*
Build fails under Fedora 23 (4.3.3-303.fc23.x86_64). Perl is 5.22.1 (system), gcc is 5.3.1 (system).
`perl Build.PL`
runs cleanly.
Output from
`perl Build build`
is shown at the end. Compilation dies on:
`cc1: error: -Wformat-security ignored without -Wformat [-Werror=format-security]`
It seems to be due to a clash between an option set in Build.PL and options originating in Config_heavy.pm.
Changing -Werror=format-security to -Wno-error=format-security, leads to different compilation errors:
`<command-line>:0:12: error: expected ')' before numeric constant`
occurring twice.
---
Complete compilation output:
`Building Bio-DB-HTS
gcc -I/opt/ghpc/include/htslib -I/usr/lib64/perl5/CORE -DVERSION="2.3" -DXS_VERSION="2.3" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wformat=0 -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=native -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c
cc1: error: -Wformat-security ignored without -Wformat [-Werror=format-security]
cc1: some warnings being treated as errors
error building lib/Bio/DB/HTS/Faidx.o from 'lib/Bio/DB/HTS/Faidx.c' at /usr/share/perl5/vendor_perl/ExtUtils/CBuilder/Base.pm line 174.`
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/62htslib 1.3.1 (and older) non-compatible header_read for SAM2018-03-16T12:04:18ZMarek Szubahtslib 1.3.1 (and older) non-compatible header_read for SAM*Created by: avullo*
I've recently addressed #54, which involved seeking at the beginning of the buffer not only for BAM/CRAM but for SAM files as well, using a dedicated function call (hseek).
This works well for htslib >= 1.5, but ...*Created by: avullo*
I've recently addressed #54, which involved seeking at the beginning of the buffer not only for BAM/CRAM but for SAM files as well, using a dedicated function call (hseek).
This works well for htslib >= 1.5, but generates segmentation faults for v1.3.1 and probably before.
I could see the hseek code in htslib has changed since then: there are some guards acting in special circumstances in the newer versions using hFILE attributes which are not defined in the older versions, but cannot say this is the cause for sure.
This is a problem which is preventing deployment of the upcoming v2.10 in the ensembl web environment, as they rely on htslib 1.3.1 (to support GRCh37 with samtools): the SAM file tests exit unexpectedly so they are deemed to fail. Obviously, this is affecting any installation which ties to htslib < 1.5.
Am I calling hseek correctly with htslib < 1.5.?
https://github.com/Ensembl/Bio-DB-HTS/blob/master/lib/Bio/DB/HTS.xs#L496
I cannot see why not.
The current workaround has just the goal of avoiding seg faults and make the tests pass with htslib 1.3.1 and older. Unfortunately, this exposes #54 again in these cases.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/30Split HTSLIB_DIR into HTSLIB_LIBDIR and HTSLIB_INCDIR2016-12-07T16:47:00ZMarek SzubaSplit HTSLIB_DIR into HTSLIB_LIBDIR and HTSLIB_INCDIR*Created by: mmokrejs*
Hi,
I am trying to create a package into Gentoo Linux.
The current INSTALL.pl logic does not work on Gentoo Linux, which tries to get around the samtools/htslib mess by installing the headers and libs into su...*Created by: mmokrejs*
Hi,
I am trying to create a package into Gentoo Linux.
The current INSTALL.pl logic does not work on Gentoo Linux, which tries to get around the samtools/htslib mess by installing the headers and libs into subdirectories (see at the end for a list of files). This setup is not detected by your INSTALL.pl script. Here is what happens:
```
>>> Emerging (1 of 1) dev-perl/Bio-DB-HTS-2.3::science
* Bio-DB-HTS-2.3.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ]
>>> Unpacking source...
>>> Unpacking Bio-DB-HTS-2.3.tar.gz to /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work
>>> Source unpacked in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work
>>> Preparing source in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work/Bio-DB-HTS-2.3 ...
>>> Source prepared.
>>> Configuring source in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work/Bio-DB-HTS-2.3 ...
* Using Module::Build
* perl Build.PL --installdirs=vendor --libdoc= --destdir=/scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/image/ --create_packlist=1
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 hts.h and libhts.a 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/local, /usr/share, /opt/local
* ERROR: dev-perl/Bio-DB-HTS-2.3::science failed (configure phase):
>>> Emerging (1 of 1) dev-perl/Bio-DB-HTS-2.3::science
* Bio-DB-HTS-2.3.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ]
>>> Unpacking source...
>>> Unpacking Bio-DB-HTS-2.3.tar.gz to /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work
>>> Source unpacked in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work
>>> Preparing source in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work/Bio-DB-HTS-2.3 ...
>>> Source prepared.
>>> Configuring source in /scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/work/Bio-DB-HTS-2.3 ...
* Using Module::Build
* perl Build.PL --installdirs=vendor --libdoc= --destdir=/scratch/var/tmp/portage/dev-perl/Bio-DB-HTS-2.3/image/ --create_packlist=1
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 hts.h and libhts.a 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/local, /usr/share, /opt/local
* ERROR: dev-perl/Bio-DB-HTS-2.3::science failed (configure phase):
```
Here is a list of files from htslib and their installation place:
```
# equery files htslib
* Searching for htslib ...
* Contents of sci-libs/htslib-1.3:
/usr
/usr/bin
/usr/bin/bgzip
/usr/bin/htsfile
/usr/bin/tabix
/usr/include
/usr/include/htslib
/usr/include/htslib/bgzf.h
/usr/include/htslib/cram.h
/usr/include/htslib/faidx.h
/usr/include/htslib/hfile.h
/usr/include/htslib/hts.h
/usr/include/htslib/hts_defs.h
/usr/include/htslib/kbitset.h
/usr/include/htslib/kfunc.h
/usr/include/htslib/khash.h
/usr/include/htslib/khash_str2int.h
/usr/include/htslib/klist.h
/usr/include/htslib/knetfile.h
/usr/include/htslib/kseq.h
/usr/include/htslib/ksort.h
/usr/include/htslib/kstring.h
/usr/include/htslib/regidx.h
/usr/include/htslib/sam.h
/usr/include/htslib/synced_bcf_reader.h
/usr/include/htslib/tbx.h
/usr/include/htslib/vcf.h
/usr/include/htslib/vcf_sweep.h
/usr/include/htslib/vcfutils.h
/usr/lib
/usr/lib/debug
/usr/lib/debug/usr
/usr/lib/debug/usr/bin
/usr/lib/debug/usr/bin/bgzip.debug
/usr/lib/debug/usr/bin/htsfile.debug
/usr/lib/debug/usr/bin/tabix.debug
/usr/lib/debug/usr/lib64
/usr/lib/debug/usr/lib64/libhts.so.1.3.debug
/usr/lib64
/usr/lib64/libhts.so -> libhts.so.1.3
/usr/lib64/libhts.so.1 -> libhts.so.1.3
/usr/lib64/libhts.so.1.3
/usr/lib64/pkgconfig
/usr/lib64/pkgconfig/htslib.pc
/usr/share
/usr/share/doc
/usr/share/doc/htslib-1.3
/usr/share/doc/htslib-1.3/NEWS.bz2
/usr/share/doc/htslib-1.3/README.bz2
/usr/share/man
/usr/share/man/man1
/usr/share/man/man1/htsfile.1.bz2
/usr/share/man/man1/tabix.1.bz2
/usr/share/man/man5
/usr/share/man/man5/faidx.5.bz2
/usr/share/man/man5/sam.5.bz2
/usr/share/man/man5/vcf.5.bz2
```
Maybe I could pursue the `PKG_CONFIG_PATH` way?
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/60HTSfile::reindex with CRAM: renaming after sorting expects BAM2018-03-06T10:05:06ZMarek SzubaHTSfile::reindex with CRAM: renaming after sorting expects BAM*Created by: avullo*
See https://github.com/Ensembl/Bio-DB-HTS/issues/57#issuecomment-364239492*Created by: avullo*
See https://github.com/Ensembl/Bio-DB-HTS/issues/57#issuecomment-364239492https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/66Add memory leak cases to test suite2018-03-20T15:22:18ZMarek SzubaAdd memory leak cases to test suite*Created by: avullo*
The latest, more comprehensive, travis builds have exposed some memory leaks which occur when releasing memory of an index. Ensure these and other types do not occur by adding appropriate tests, e.g. using Test::Lea...*Created by: avullo*
The latest, more comprehensive, travis builds have exposed some memory leaks which occur when releasing memory of an index. Ensure these and other types do not occur by adding appropriate tests, e.g. using Test::LeakTrace.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/63Travis to test with multiple htslib versions2018-03-14T17:06:18ZMarek SzubaTravis to test with multiple htslib versions*Created by: avullo*
Both ensembl web and vep rely on htslib 1.3.1, but development and enhancements are tied to newer library versions. So far, we've observed installation issues and also some header reading incompatibilities, see e.g....*Created by: avullo*
Both ensembl web and vep rely on htslib 1.3.1, but development and enhancements are tied to newer library versions. So far, we've observed installation issues and also some header reading incompatibilities, see e.g. #62 and #54.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/57Does not support csi index2018-03-05T17:15:27ZMarek SzubaDoes not support csi index*Created by: keiranmraine*
The perl code doesn't handle the more efficient `csi` index for bam files:
https://github.com/Ensembl/Bio-DB-HTS/blob/master/lib/Bio/DB/HTS.pm#L2146*Created by: keiranmraine*
The perl code doesn't handle the more efficient `csi` index for bam files:
https://github.com/Ensembl/Bio-DB-HTS/blob/master/lib/Bio/DB/HTS.pm#L2146https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/55BCF indexing2018-04-16T15:50:47ZMarek SzubaBCF indexing*Created by: rishidev*
It would be good to be able to have the ability to jump straight into an indexed BCF file, perhaps using the bcf_sr_seek function in HTSlib.*Created by: rishidev*
It would be good to be able to have the ability to jump straight into an indexed BCF file, perhaps using the bcf_sr_seek function in HTSlib.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/59Archives install script tied to master2018-03-15T14:35:28ZMarek SzubaArchives install script tied to master*Created by: avullo*
The install script for previous releases downloads and builds the master branch code.
An excerpt from running it for 2.7, showing how it is bound to the current release number as set in master (2.9):
*** Buildin...*Created by: avullo*
The install script for previous releases downloads and builds the master branch code.
An excerpt from running it for 2.7, showing how it is bound to the current release number as set in master (2.9):
*** Building Bio::DB::HTS ***
***CMD*** : env HTSLIB_DIR=/tmp/lCFQHly_Rz/htslib perl Build.PL
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Bio-DB-HTS' version '2.9'
Building Bio-DB-HTS
cc -I/tmp/lCFQHly_Rz/htslib/htslib -I/home/avullo/perl5/perlbrew/perls/perl-5.16.0/lib/5.16.0/x86_64-linux/CORE -DXS_VERSION="2.9" -DVERSION="2.9" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs')
...
This is about introducing a version variable in the install script, and keeping it in sync at release time with the version number as set in the various modules.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/Bio-DB-HTS/-/issues/14Functionality to write bam file2016-05-19T09:39:20ZMarek SzubaFunctionality to write bam file*Created by: sb43*
Would be handy to have method available in bio::db::sam that writes bam file.
*Created by: sb43*
Would be handy to have method available in bio::db::sam that writes bam file.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/44The install script fails with GNU Wget 1.122017-06-17T13:09:49ZMarek SzubaThe install script fails with GNU Wget 1.12*Created by: dbolser-ebi*
I don't know why, but this version of wget trims off the file extension while downloading, breaking the logic of the install script:
```
[dbolser@gunpowder Bio-DB-HTS]$ perl INSTALL.pl --prefix $PWD/build
/n...*Created by: dbolser-ebi*
I don't know why, but this version of wget trims off the file extension while downloading, breaking the logic of the install script:
```
[dbolser@gunpowder Bio-DB-HTS]$ perl INSTALL.pl --prefix $PWD/build
/nfs/production/panda/ensemblgenomes/development/dbolser/Web/Ensembl/Test_Ensembl_89/Bio-DB-HTS
*** Performing build in /tmp/PrkgGdxgMT ***
*** Checking out HTSlib v1.3.1 ***
1.3.1.zip
--2017-06-16 10:53:32-- https://github.com/samtools/htslib/archive/1.3.1.zip
Resolving github.com... 192.30.253.113, 192.30.253.112
Connecting to github.com|192.30.253.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/samtools/htslib/zip/1.3.1 [following]
--2017-06-16 10:53:32-- https://codeload.github.com/samtools/htslib/zip/1.3.1
Resolving codeload.github.com... 192.30.253.121, 192.30.253.120
Connecting to codeload.github.com|192.30.253.121|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1170333 (1.1M) [application/zip]
Saving to: `1.3.1'
100%[================================================================================================>] 1,170,333 1.47M/s in 0.8s
2017-06-16 10:53:34 (1.47 MB/s) - `1.3.1' saved [1170333/1170333]
Could not fetch HTSlib archive https://github.com/samtools/htslib/archive/1.3.1.zip at INSTALL.pl line 104.
```
There is probably a library to abstract downloads in Perl.https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/46Switch to using hisremote2017-06-17T13:09:01ZMarek SzubaSwitch to using hisremote*Created by: andrewyatz*
Currently Bio::HTS::Lib has its own routine for deciding if a given location is a remote or locally hosted file. htslib now has `hisremote()`, which does the same thing. We should switch to using this routine ra...*Created by: andrewyatz*
Currently Bio::HTS::Lib has its own routine for deciding if a given location is a remote or locally hosted file. htslib now has `hisremote()`, which does the same thing. We should switch to using this routine rather than using our own versionhttps://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/27system exit codes not checked - silent install failures2016-08-04T10:50:27ZMarek Szubasystem exit codes not checked - silent install failures*Created by: keiranmraine*
The system calls aren't being checked. Causes specific issues on minimal installs if `wget` not present:
https://github.com/Ensembl/Bio-HTS/blob/master/INSTALL.pl#L83
*Created by: keiranmraine*
The system calls aren't being checked. Causes specific issues on minimal installs if `wget` not present:
https://github.com/Ensembl/Bio-HTS/blob/master/INSTALL.pl#L83
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/2Looking for some examples of basic FASTA/Q handling with Bio::DB::HTS2016-05-25T08:20:21ZMarek SzubaLooking for some examples of basic FASTA/Q handling with Bio::DB::HTS*Created by: sestaton*
First, thanks for the work on this and for making it available on CPAN. I would like to know if there are any plans to add bindings to the FASTA/Q parsing methods in kseq.h of htslib? This may be possible already ...*Created by: sestaton*
First, thanks for the work on this and for making it available on CPAN. I would like to know if there are any plans to add bindings to the FASTA/Q parsing methods in kseq.h of htslib? This may be possible already or by some other method but it is not clear. For reference, @cjfields has already written bindings to kseq.h in the [Bio::Kseq](https://github.com/cjfields/Bio-Kseq) module, which is extremely useful because it is much faster than any pure-Perl parser. I think it would be great to have those basic sequence reading methods in one package along with all the alignment methods.
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/28Does Bio-HTS use ENA for CRAM tests?2016-10-20T10:59:03ZMarek SzubaDoes Bio-HTS use ENA for CRAM tests?*Created by: andrewyatz*
I've seen some odd behaviour running tests on the Ensembl REST API. It seems that travis build failed because of issues with accessing ENA (I've been told this but have not verified the problem). Do we go to ENA...*Created by: andrewyatz*
I've seen some odd behaviour running tests on the Ensembl REST API. It seems that travis build failed because of issues with accessing ENA (I've been told this but have not verified the problem). Do we go to ENA for any entries in the CRAM registry or do we always use the locally available FASTA file?
If we do then we should either make it an optional test pending if CRAM registry is available or switch to using a local file system or mock HTTP server using [Test::Fake::HTTPD](http://search.cpan.org/~masaki/Test-Fake-HTTPD/README.pod). There's a good example of how to configure it in the [Ensembl core test suite for network downloads](https://github.com/Ensembl/ensembl/blob/release/84/modules/t/utilsNet.t#L70). Happy to lend a hand
https://gitlab.ebi.ac.uk/ensembl-gh-mirror/Bio-DB-HTS/-/issues/31Why didn't you just rename the repo?2016-08-05T12:42:08ZMarek SzubaWhy didn't you just rename the repo?*Created by: keiranmraine*
All links are maintained if you rename the repo so legacy docs just magically get redirected.
*Created by: keiranmraine*
All links are maintained if you rename the repo so legacy docs just magically get redirected.