Skip to content

Commit

Permalink
Clarification of --rf, --ff options
Browse files Browse the repository at this point in the history
  • Loading branch information
pd3 committed Oct 26, 2021
1 parent 86ce2a4 commit 756e636
Show file tree
Hide file tree
Showing 2 changed files with 5 additions and 5 deletions.
6 changes: 3 additions & 3 deletions doc/bcftools.txt
Original file line number Diff line number Diff line change
Expand Up @@ -1901,7 +1901,7 @@ those scenarios.
*-Q, --min-BQ* 'INT'::
Minimum base quality for a base to be considered [13]

* --max-BQ* 'INT'::
*--max-BQ* 'INT'::
Caps the base quality to a maximum value [60]. This can be
particularly useful on technologies that produce overly optimistic
high qualities, leading to too many false positives or incorrect
Expand All @@ -1920,10 +1920,10 @@ those scenarios.
Ignore RG tags. Treat all reads in one alignment file as one sample.

*--rf, --incl-flags* 'STR'|'INT'::
Required flags: skip reads with mask bits unset [null]
Required flags: skip reads with none of the mask bits set [null]

*--ff, --excl-flags* 'STR'|'INT'::
Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]
Filter flags: skip reads with any of the mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]

*-s, --samples* [^]'LIST'::
list of sample names. See *<<common_options,Common Options>>*
Expand Down
4 changes: 2 additions & 2 deletions mpileup.c
Original file line number Diff line number Diff line change
Expand Up @@ -1122,9 +1122,9 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
" -r, --regions REG[,...] Comma separated list of regions in which pileup is generated\n"
" -R, --regions-file FILE Restrict to regions listed in a file\n"
" --ignore-RG Ignore RG tags (one BAM = one sample)\n"
" --rf, --incl-flags STR|INT Required flags: skip reads with mask bits unset [%s]\n", tmp_require);
" --rf, --incl-flags STR|INT Required flags: skip reads with none of the bits set [%s]\n", tmp_require);
fprintf(fp,
" --ff, --excl-flags STR|INT Filter flags: skip reads with mask bits set\n"
" --ff, --excl-flags STR|INT Filter flags: skip reads with any of the bits set\n"
" [%s]\n", tmp_filter);
fprintf(fp,
" -s, --samples LIST Comma separated list of samples to include\n"
Expand Down

0 comments on commit 756e636

Please sign in to comment.