Martin Mokrejš

Hi, could the following error message be improved to print out the "wrong" query name? ``` bamsort SO=coordinate blockmb=96000 inputthreads=1 outputthreads=1 level=9 index=1 I=tadpole.k62.shave.rinse.bam O=tadpole.k62.shave.rinse.sorted.bam [V] Reading alignments from source....

bammerge: Accept wildcard regexp when parsing I= input

2

It is confusing that bammerge wants to write on STDOUT. I think is is a very bad idea because the shell redirect will buffer the data and for example if...

Hi, I am new to using this tool (2.0.69) but find it weird why commandline arguments are not systematically shared or why some apllications lack arguments supposedly common to your...

0.6.0: AttributeError: 'Fast5File' object has no attribute 'read_metadata'

3

``` $ poretools metadata foo_26553_ch307_read1591_strand.fast5 asic_id asic_temp heatsink_temp 151059866 30.9320774 34.2539063 $ poretools metadata --read foo_26553_ch307_read1591_strand.fast5 Traceback (most recent call last): File "/apps/gentoo/usr/lib/python-exec/python2.7/poretools", line 11, in load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')() File...

0.6.0: TypeError: int() argument must be a string or a number, not 'NoneType'

1

Hi, I cannot get any of the plotting functions to work. All of them crash with: ``` $ poretools yield_plot --plot-type reads */*.fast5 Traceback (most recent call last): File "/apps/gentoo/usr/lib/python-exec/python2.7/poretools",...

configure forces -std=c++98 but that should be moved to relevant Makefiles or sga code adjusted

6

For me configure does not detect sparsehash-2.0.3 not even with current git master at commit af73db617738ff3e4c85cb370f485b208d6be15c : ``` ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64...

Hi, I am trying to improve georeferencing of some large TIF but the plugin prints an info message `Georeferencing loaded : Found existing georeferencing in raster` but then the image...