Clarify what -U does

See #424

Author: marcelm

README.md

@@ -158,7 +158,8 @@ options. Some important ones are:
   specified multiple times. Example: `--rg-id=1 --rg=SM:mysamle --rg=LB:mylibrary`.
 * `-N INT`: Output up to INT secondary alignments. By default, no secondary
   alignments are output.
-* `-U`: Suppress output of unmapped reads.
+* `-U`: Suppress output of unmapped single-end reads and pairs in which both
+  reads are unmapped.
 * `--use-index`: Use a pre-generated index instead of generating a new one.
 * `--create-index`, `-i`: Generate a strobemer index file (`.sti`) and write it
   to disk next to the input reference FASTA. Do not map reads. If read files are

src/cmdline.cpp

@@ -36,7 +36,7 @@ CommandLineOptions parse_command_line_arguments(int argc, char **argv) {
     args::Group sam(parser, "SAM output:");
     args::Flag eqx(parser, "eqx", "Emit =/X instead of M CIGAR operations", {"eqx"});
     args::Flag no_pg(parser, "no-PG", "Do not output PG header", {"no-PG"});
-    args::Flag U(parser, "U", "Suppress output of unmapped reads", {'U'});
+    args::Flag U(parser, "U", "Do not output unmapped single-end reads. Do not output pairs where both reads are unmapped", {'U'});
     args::ValueFlag<std::string> rgid(parser, "ID", "Read group ID", {"rg-id"});
     args::ValueFlagList<std::string> rg(parser, "TAG:VALUE", "Add read group metadata to SAM header (can be specified multiple times). Example: SM:samplename", {"rg"});
     args::Flag details(parser, "details", "Add debugging details to SAM records", {"details"});