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write hits to tmp files (unfinished)

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Heng Li
2018-07-14 12:15:10 -04:00
parent 5cfa621b2d
commit 1a55227d5a
8 changed files with 103 additions and 31 deletions
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main.c
+2
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@@ -61,6 +61,7 @@ static struct option long_options[] = {
{ "score-N", required_argument, 0, 0 }, // 31
{ "eqx", no_argument, 0, 0 }, // 32
{ "paf-no-hit", no_argument, 0, 0 }, // 33
{ "split-prefix", required_argument, 0, 0 }, // 34
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -181,6 +182,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==31) opt.sc_ambi = atoi(optarg); // --score-N
else if (c == 0 && long_idx ==32) opt.flag |= MM_F_EQX; // --eqx
else if (c == 0 && long_idx ==33) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
else if (c == 0 && long_idx ==34) opt.split_prefix = optarg; // --split-prefix
else if (c == 0 && long_idx == 14) { // --frag
yes_or_no(&opt, MM_F_FRAG_MODE, long_idx, optarg, 1);
} else if (c == 0 && long_idx == 15) { // --secondary