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https://github.com/google-deepmind/alphafold3.git
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751a4b8612
* See https://github.com/EddyRivasLab/hmmer/issues/323 for more context. * We observed 75.6 GB -> 13.6 GB peak RAM reduction for one of our queries. PiperOrigin-RevId: 782808687 Change-Id: I4306dc6921015c88c5f8ced69a4ef46e10574a57
33 lines
3.3 KiB
Diff
33 lines
3.3 KiB
Diff
--- hmmer-3.4/src/jackhmmer.c
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+++ hmmer-3.4/src/jackhmmer.c
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@@ -73,6 +73,7 @@ static ESL_OPTIONS options[] = {
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{ "--noali", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "don't output alignments, so output is smaller", 2 },
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{ "--notextw", eslARG_NONE, NULL, NULL, NULL, NULL, NULL, "--textw", "unlimit ASCII text output line width", 2 },
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{ "--textw", eslARG_INT, "120", NULL, "n>=120", NULL, NULL, "--notextw", "set max width of ASCII text output lines", 2 },
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+ { "--seq_limit", eslARG_INT, NULL, NULL, NULL, NULL, NULL, "--seq_limit", "if set, truncate all hits after this value is reached", 2 },
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/* Control of scoring system */
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{ "--popen", eslARG_REAL, "0.02", NULL, "0<=x<0.5",NULL, NULL, NULL, "gap open probability", 3 },
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{ "--pextend", eslARG_REAL, "0.4", NULL, "0<=x<1", NULL, NULL, NULL, "gap extend probability", 3 },
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@@ -298,6 +299,7 @@ output_header(FILE *ofp, ESL_GETOPTS *go
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if (esl_opt_IsUsed(go, "--noali") && fprintf(ofp, "# show alignments in output: no\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
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if (esl_opt_IsUsed(go, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimited\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
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if (esl_opt_IsUsed(go, "--textw") && fprintf(ofp, "# max ASCII text line length: %d\n", esl_opt_GetInteger(go, "--textw")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
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+ if (esl_opt_IsUsed(go, "--seq_limit") && fprintf(ofp, "# set max sequence hits to return: %d\n", esl_opt_GetInteger(go, "--seq_limit")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
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if (esl_opt_IsUsed(go, "--popen") && fprintf(ofp, "# gap open probability: %f\n", esl_opt_GetReal (go, "--popen")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
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if (esl_opt_IsUsed(go, "--pextend") && fprintf(ofp, "# gap extend probability: %f\n", esl_opt_GetReal (go, "--pextend")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
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if (esl_opt_IsUsed(go, "--mx") && fprintf(ofp, "# subst score matrix (built-in): %s\n", esl_opt_GetString (go, "--mx")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
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@@ -674,6 +676,13 @@ serial_master(ESL_GETOPTS *go, struct cf
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/* Print the results. */
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p7_tophits_SortBySortkey(info->th);
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p7_tophits_Threshold(info->th, info->pli);
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+ /* Limit the number of hits if specified. */
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+ if (esl_opt_IsOn(go, "--seq_limit"))
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+ {
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+ int seq_limit = esl_opt_GetInteger(go, "--seq_limit");
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+ info->th->N = ESL_MIN(info->th->N, seq_limit);
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+ }
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+
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p7_tophits_CompareRanking(info->th, kh, &nnew_targets);
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p7_tophits_Targets(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
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p7_tophits_Domains(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
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