Update paths in bwa-mem2-lisa

[aawdeh]

Hi!

I have been trying to compile and run bwa-mem2-lisa with no success. As a result, to get it to work, I added/modified the following lines -- customizing the paths to match my directory. However, in order to ensure its functionality for others, these paths would need to be made more general. For context, my OS is a Debian GNU/Linux 11 (bullseye).

Please find below the changes I made below:

1. Moved the lz to the end of line 59 in the Makefile in bwa-mem2-lisa/ext/TAL

sed -i '44s/.*/LIBS=-fopenmp -lm -L. -ltal -Lext\/safestringlib\/ -lsafestring -lz/' Makefile

2. Added full paths to make sure the program knows where to look -- more specifically, to lines 52, 53, 455 and 704 in /ext/TAL/src/LISA-FMI/ipbwt_rmi.h and line 19 in /ext/TAL/scripts/build-rmi.linear_spline.linear.sh. The path /usr/gitc/temp/bwa-mem2-lisa is specific to my environment -- and thus would need to be modified.

Line 52: IPBWT_RMI(const string &t, string ref_seq_filename, int K_, int64_t num_rmi_leaf_nodes, index_t *__sa = NULL, string lisa_home = "/usr/gitc/temp/bwa-mem2-lisa“);

Line 53: IPBWT_RMI(const string &t, index_t t_size, string ref_seq_filename, int K_, int64_t num_rmi_leaf_nodes, index_t *__sa = NULL, string lisa_home = "/usr/gitc/temp/bwa-mem2-lisa”);

Line 455: string shell_cmd = "cd " + lisa_home + "&& bash /usr/gitc/temp/bwa-mem2-lisa/ext/TAL/scripts/build-rmi.linear_spline.linear.sh " + ipbwt_f64_filename + " " + rmi_filename + " " + to_string(num_rmi_leaf_nodes) + " " + "F64”;

Line 704: string shell_cmd = "/usr/gitc/temp/bwa-mem2-lisa/ext/TAL/scripts/build-rmi.linear_spline.linear.sh " + ipbwt_f64_filename + " " + rmi_filename + " " + to_string(num_rmi_leaf_nodes) + " " + "F64";

Line 19: cd /usr/gitc/temp/bwa-mem2-lisa/ext/build-rmi/learned-systems-rmi

Would it be possible to make the following changes to bwa-mem2-lisa?