/dports/biology/infernal/infernal-1.1.3/easel/miniapps/ |
H A D | cmd_filter.md | 23 sequence fragments (see `--fragthresh`). These rules, and options that 116 fragthresh/symfrac rules to a sample of 10K sequences instead of 140 `--fragthresh` and `--symfrac`. 154 Do not use a statistical subsample when using the fragthresh/symfrac 157 #### `--fragthresh <x>` 167 fragthresh calculations, without affecting the alignment itself. 169 The smaller `fragthresh` is, the fewer fragments are defined. 170 `--fragthresh 0` says no sequences are fragments. `--fragthresh 1`
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H A D | cmd_filter.c | 72 cfg->fragthresh = esl_opt_GetReal (go, "--fragthresh"); in esl_cmd_filter()
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/dports/biology/hmmer/hmmer-3.3/easel/miniapps/ |
H A D | cmd_filter.md | 23 sequence fragments (see `--fragthresh`). These rules, and options that 116 fragthresh/symfrac rules to a sample of 10K sequences instead of 140 `--fragthresh` and `--symfrac`. 154 Do not use a statistical subsample when using the fragthresh/symfrac 157 #### `--fragthresh <x>` 167 fragthresh calculations, without affecting the alignment itself. 169 The smaller `fragthresh` is, the fewer fragments are defined. 170 `--fragthresh 0` says no sequences are fragments. `--fragthresh 1`
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H A D | cmd_filter.c | 72 cfg->fragthresh = esl_opt_GetReal (go, "--fragthresh"); in esl_cmd_filter()
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/dports/biology/infernal/infernal-1.1.3/easel/ |
H A D | esl_msa.h | 177 extern int esl_msa_MarkFragments (const ESL_MSA *msa, float fragthresh, ESL_BITFIELD **ret_fragassi… 178 extern int esl_msa_MarkFragments_old(ESL_MSA *msa, double fragthresh);
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H A D | esl_msaweight.h | 16 …float fragthresh; // seq is a fragment if (length from 1st to last aligned residue)/alen < fra… member
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H A D | esl_msaweight.c | 313 float fragthresh = (cfg? cfg->fragthresh : eslMSAWEIGHT_FRAGTHRESH); in consensus_by_sample() local 334 …minspan = (int) ceil( fragthresh * (float) msa->alen ); // define alispan as aligned length fr… in consensus_by_sample() 426 …float fragthresh = (cfg? cfg->fragthresh : eslMSAWEIGHT_FRAGTHRESH); // seq is fragment if (l… in collect_counts() local 427 …int minspan = (int) ceil( fragthresh * (float) msa->alen ); // precalculated span le… in collect_counts() 552 cfg->fragthresh = eslMSAWEIGHT_FRAGTHRESH; in esl_msaweight_cfg_Create() 1808 cfg->fragthresh = esl_opt_GetReal (go, "--fragthresh"); in main() 1839 printf("# fragthresh: %.4f\n", cfg->fragthresh); in main()
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H A D | esl_msa.c | 2133 esl_msa_MarkFragments(const ESL_MSA *msa, float fragthresh, ESL_BITFIELD **ret_fragassign) in esl_msa_MarkFragments() argument 2136 …int minspan = (int) ceil(fragthresh * (float) msa->alen); // precalculated span lengt… in esl_msa_MarkFragments() 2205 esl_msa_MarkFragments_old(ESL_MSA *msa, double fragthresh) in esl_msa_MarkFragments_old() argument 2211 if (msa_get_rlen(msa, i) <= fragthresh * msa->alen) in esl_msa_MarkFragments_old()
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/dports/biology/hmmer/hmmer-3.3/easel/ |
H A D | esl_msa.h | 177 extern int esl_msa_MarkFragments (const ESL_MSA *msa, float fragthresh, ESL_BITFIELD **ret_fragassi… 178 extern int esl_msa_MarkFragments_old(ESL_MSA *msa, double fragthresh);
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H A D | esl_msaweight.h | 16 …float fragthresh; // seq is a fragment if (length from 1st to last aligned residue)/alen < fra… member
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H A D | esl_msaweight.c | 313 float fragthresh = (cfg? cfg->fragthresh : eslMSAWEIGHT_FRAGTHRESH); in consensus_by_sample() local 334 …minspan = (int) ceil( fragthresh * (float) msa->alen ); // define alispan as aligned length fr… in consensus_by_sample() 426 …float fragthresh = (cfg? cfg->fragthresh : eslMSAWEIGHT_FRAGTHRESH); // seq is fragment if (l… in collect_counts() local 427 …int minspan = (int) ceil( fragthresh * (float) msa->alen ); // precalculated span le… in collect_counts() 552 cfg->fragthresh = eslMSAWEIGHT_FRAGTHRESH; in esl_msaweight_cfg_Create() 1808 cfg->fragthresh = esl_opt_GetReal (go, "--fragthresh"); in main() 1839 printf("# fragthresh: %.4f\n", cfg->fragthresh); in main()
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H A D | esl_msa.c | 2133 esl_msa_MarkFragments(const ESL_MSA *msa, float fragthresh, ESL_BITFIELD **ret_fragassign) in esl_msa_MarkFragments() argument 2136 …int minspan = (int) ceil(fragthresh * (float) msa->alen); // precalculated span lengt… in esl_msa_MarkFragments() 2205 esl_msa_MarkFragments_old(ESL_MSA *msa, double fragthresh) in esl_msa_MarkFragments_old() argument 2211 if (msa_get_rlen(msa, i) <= fragthresh * msa->alen) in esl_msa_MarkFragments_old()
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/dports/multimedia/v4l_compat/linux-5.13-rc2/drivers/net/wireless/broadcom/brcm80211/brcmsmac/ |
H A D | main.h | 540 u16 fragthresh[NFIFO]; member
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H A D | main.c | 4325 wlc->fragthresh[i] = DOT11_DEFAULT_FRAG_LEN; in brcms_c_info_init() 6774 if (wlc->fragthresh[queue] != in brcms_c_d11hdrs_mac80211() 6776 wlc->fragthresh[queue] = in brcms_c_d11hdrs_mac80211() 6790 phylen, wlc->fragthresh[queue], in brcms_c_d11hdrs_mac80211()
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/dports/multimedia/v4l-utils/linux-5.13-rc2/drivers/net/wireless/broadcom/brcm80211/brcmsmac/ |
H A D | main.h | 540 u16 fragthresh[NFIFO]; member
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H A D | main.c | 4325 wlc->fragthresh[i] = DOT11_DEFAULT_FRAG_LEN; in brcms_c_info_init() 6774 if (wlc->fragthresh[queue] != in brcms_c_d11hdrs_mac80211() 6776 wlc->fragthresh[queue] = in brcms_c_d11hdrs_mac80211() 6790 phylen, wlc->fragthresh[queue], in brcms_c_d11hdrs_mac80211()
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/dports/multimedia/libv4l/linux-5.13-rc2/drivers/net/wireless/broadcom/brcm80211/brcmsmac/ |
H A D | main.h | 540 u16 fragthresh[NFIFO]; member
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H A D | main.c | 4325 wlc->fragthresh[i] = DOT11_DEFAULT_FRAG_LEN; in brcms_c_info_init() 6774 if (wlc->fragthresh[queue] != in brcms_c_d11hdrs_mac80211() 6776 wlc->fragthresh[queue] = in brcms_c_d11hdrs_mac80211() 6790 phylen, wlc->fragthresh[queue], in brcms_c_d11hdrs_mac80211()
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/dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
H A D | p7_builder.c | 109 bld->fragthresh = (go != NULL) ? esl_opt_GetReal (go, "--fragthresh") : 0.5; in p7_builder_Create() 427 if ((status = esl_msa_MarkFragments_old(msa, bld->fragthresh)) != eslOK) goto ERROR; in p7_Builder()
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H A D | hmmer.h | 1269 float fragthresh; /* if L <= fragthresh*alen, seq is called a fragment */ member
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/dports/biology/hmmer/hmmer-3.3/src/ |
H A D | p7_builder.c | 109 bld->fragthresh = (go != NULL) ? esl_opt_GetReal (go, "--fragthresh") : 0.5; in p7_builder_Create() 427 if ((status = esl_msa_MarkFragments_old(msa, bld->fragthresh)) != eslOK) goto ERROR; in p7_Builder()
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H A D | hmmer.h | 1269 float fragthresh; /* if L <= fragthresh*alen, seq is called a fragment */ member
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/dports/biology/infernal/infernal-1.1.3/hmmer/testsuite/ |
H A D | testsuite.sqc | 110 1 exercise build/--fragthresh @src/hmmbuild@ --fragthresh 0.4 --EmL 10 --EvL 10 --EfL 10 %HMMB…
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/dports/biology/hmmer/hmmer-3.3/testsuite/ |
H A D | testsuite.sqc | 110 1 exercise build/--fragthresh @src/hmmbuild@ --fragthresh 0.4 --EmL 10 --EvL 10 --EfL 10 %HMMB…
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