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Add "bwa mem -o FILE" synonym and documentation 

As -o is still free in the mem command, use that standard option to
specify an output file (and keep -f to parallel bwase/bwape commands).
Document it in the usage and man page.
This commit is contained in:
John Marshall 2017-06-27 17:05:44 +01:00
parent d28da05f36
commit bc58bf265d
2 changed files with 11 additions and 2 deletions
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8
bwa.1
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@ -277,6 +277,14 @@ If ARG starts with @, it is interpreted as a string and gets inserted into the
output SAM header; otherwise, ARG is interpreted as a file with all lines
starting with @ in the file inserted into the SAM header. [null]
.TP
.BI -o \ FILE
Write the output SAM file to
.IR FILE .
For compatibility with other BWA commands, this option may also be given as
.B -f
.IR FILE .
[standard ouptut]
.TP
.BI -T \ INT
Don't output alignment with score lower than
.IR INT .

5
fastmap.c
View File

@ -130,7 +130,7 @@ int main_mem(int argc, char *argv[])
aux.opt = opt = mem_opt_init();
memset(&opt0, 0, sizeof(mem_opt_t));
while ((c = getopt(argc, argv, "51paMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:f:W:x:G:h:y:K:X:H:")) >= 0) {
while ((c = getopt(argc, argv, "51paMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:o:f:W:x:G:h:y:K:X:H:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
else if (c == '1') no_mt_io = 1;
else if (c == 'x') mode = optarg;
@ -158,7 +158,7 @@ int main_mem(int argc, char *argv[])
else if (c == 's') opt->split_width = atoi(optarg), opt0.split_width = 1;
else if (c == 'G') opt->max_chain_gap = atoi(optarg), opt0.max_chain_gap = 1;
else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1;
else if (c == 'f') xreopen(optarg, "wb", stdout);
else if (c == 'o' || c == 'f') xreopen(optarg, "wb", stdout);
else if (c == 'W') opt->min_chain_weight = atoi(optarg), opt0.min_chain_weight = 1;
else if (c == 'y') opt->max_mem_intv = atol(optarg), opt0.max_mem_intv = 1;
else if (c == 'C') aux.copy_comment = 1;
@ -266,6 +266,7 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, " -p smart pairing (ignoring in2.fq)\n");
fprintf(stderr, " -R STR read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
fprintf(stderr, " -H STR/FILE insert STR to header if it starts with @; or insert lines in FILE [null]\n");
fprintf(stderr, " -o FILE sam file to output results to [stdout]\n");
fprintf(stderr, " -j treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n");
fprintf(stderr, " -5 always take the leftmost alignment on a read as primary\n");
fprintf(stderr, "\n");