hmehlan

In your case and in the tutorial, two things come together - filterBam uses the NM flag in BAM files to determine sequence identity, but theSTAR genome alignment does not...

tldr; - probably a version of HTSlib lower than 1.10 is used - see [docs/INSTALL.md](https://github.com/Gaius-Augustus/Augustus/blob/master/docs/INSTALL.md#HTSlib) for help Please check the compiler call `cc -Wall -O2 -I/usr/include/htslib -I/usr/local/include/htslib/ -c bam2wig.c` In...

It seems tempting to use pkg-config in Makefiles, but - pkg-config is not installed by default on all platforms (e.g. Windows, RHEL/CentOS) - not every library support pkg-config and provide...

Thanks for the feedback. As @mathog suggested, all INCLUDES and LIBRARY paths can now be set in [commons.mk](https://github.com/Gaius-Augustus/Augustus/blob/master/common.mk) alone. Help with problems or hints for installing necessary packages as a...

Hello @MaxCoyle4, you were right in adding "/bamtools" to the INCLUDES variable, but you still missed the leading "-I". The README file missed both. Sorry. Please change your `INCLUDES =...

All INCLUDES and LIBRARY paths can be set in [commons.mk](https://github.com/Gaius-Augustus/Augustus/blob/master/common.mk). Please see the boost section in [docs/INSTALL.md](https://github.com/Gaius-Augustus/Augustus/blob/master/docs/INSTALL.md) Probably you have to set INCLUDE_PATH_BOOST (and LIBRARY_PATH_BOOST) to the correct paths in...

@aditi17142 : probably a version of HTSlib lower than 1.10 is used compare compiler output "Check if HTSlib is installed and of version 1.10 or higher" see [docs/INSTALL.md](https://github.com/Gaius-Augustus/Augustus/blob/master/docs/INSTALL.md#htslib---accessing-common-file-formats-such-as-sam-cram-and-vcf) for help...

The augustus-_version_.tar.gz files are intended as an easy way to download different AUGUSTUS versions. The binaries inside will only be executable in rare cases where, among other things, all link...

would it be possible to get a small example file along with the commands used to reproduce the problem? thank you!

possibly related: ``` $ bin/augustus --species=leishmania_tarentolae --singlestrand=true docs/tutorial/data/chr2R.fa Could not find the config file config/model/states_singlestrand_intronless.cfg. Looking for states_singlestrand_intronless.cfg in the configuration directory instead ... not found. bin/augustus: ERROR Properties::readFile: Could...