Sascha Steinbiss

Build process uses static filenames in /tmp, does not catch errors

1

The build process (`include.sh` and friends) uses static filenames in` /tmp/`, among them `/tmp/closure_error.log` which in addition does not get removed after the build. This may lead to issues on...

Failing test_vcf_api/test_vcf_sweep tests on i386

17

I'm forwarding Debian bug 865012 (https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=865012), which mentions failing tests on i386. I can reproduce these on a plain Debian stretch i386 install with the most recent htslib release 1.5:...

Some tools still rely on the `seq0`, `seq1`... naming scheme for sequence regions. For example, the LTR clustering and classification tools. They need to be adapted to use _GtRegionMapping_ input...

GFF3 escaping

18

I was just wondering whether GFF3 escaping is used in the GFF3 input/output streams at all? ``` [ss34@mib106184i:~/develop/genometools] git grep gt_gff3_escape src/extended/gff3_escaping.c:static int gt_gff3_escape_hex2prnchar(const char* str, char *out) src/extended/gff3_escaping.c:static void...

Failing tests on Linux/PPC

7

While debugging some code to get the GenomeTools Debian packages to build successfully on exotic platforms, I noticed that other tests fail as well (~150). A complete list is here:...

'tidy'ing nodes with invalid parents

5

I am thinking about the best way to deal with nodes that have invalid (i.e. dangling) `Parent` IDs. As mentioned earlier, I sometimes encounter these and they usually break any...

translation code and ambiguity handling

4

Currently, the protein translation engine sometimes makes unexpected calls when ambiguity is involved. For example, ``` $ gt -i gt (GenomeTools) 1.5.3 (2014-06-19 11:44:22) > print(gt.translate_dna("nag")) * ``` So NAG...

add API methods to extract flanking sequence for a feature node

5

While it is easy to get the sequence for a feature given a GtRegionMapping, it is sometimes desired to extract a flanking sequence, either downstream or upstream of the feature....

gt interfeat and top-level features

7

I am trying to extract intron and intergenic sequences with `gt interfeat` and `gt extractfeat`. For introns, this works nicely: ``` gt interfeat -outside CDS -inter intron annotation.gff3.gz | gt...

Make the GTF parser handle alternative CDS per transcript

4

This tool seems to create duplicate features when given a DAG as input: ``` $ bin/gt gff3_to_gtf testdata/standard_gene_as_dag.gff3 warning: skipping GFF3 feature of type "TF_binding_site" (from line 4 in file...