coverm/
external_command_checker.rs

1use bird_tool_utils::external_command_checker::*;
2
3pub fn check_for_bwa() {
4    check_for_external_command_presence("BWA", "which bwa").expect("Failed to find installed BWA");
5}
6
7pub fn check_for_bwa_mem2() {
8    check_for_external_command_presence("BWA", "which bwa-mem2")
9        .expect("Failed to find installed BWA");
10    default_version_check("bwa-mem2", "2.0", false, Some("bwa-mem2 version"))
11        .expect("Failed to find sufficient version of bwa-mem2");
12}
13
14pub fn check_for_minimap2() {
15    check_for_external_command_presence("minimap2", "which minimap2")
16        .expect("Failed to find installed minimap2");
17    default_version_check("minimap2", "2.24-r1122", false, None)
18        .expect("Failed to find sufficient version of minimap2");
19}
20
21pub fn check_for_samtools() {
22    check_for_external_command_presence("samtools", "which samtools")
23        .expect("Failed to find installed samtools");
24    default_version_check("samtools", "1.9", false, None)
25        .expect("Failed to find sufficient version of samtools");
26}
27
28pub fn check_for_strobealign() {
29    check_for_external_command_presence("strobealign", "which strobealign")
30        .expect("Failed to find installed strobealign");
31    default_version_check("strobealign", "0.11.0", false, None)
32        .expect("Failed to find sufficient version of strobealign");
33}
coverm/external_command_checker.rs

coverm/
external_command_checker.rs
