/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
H A D | bam_plcmd.c | 218 mplp_pileup_t gplp; in mpileup() local 220 memset(&gplp, 0, sizeof(mplp_pileup_t)); in mpileup() 264 gplp.n = sm->n; in mpileup() 337 for (i = 0; i < gplp.n; ++i) in mpileup() 338 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); in mpileup() 339 bcf_call_combine(gplp.n, bcr, ref16, &bc); in mpileup() 345 …NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos,… in mpileup() 346 for (i = 0; i < gplp.n; ++i) in mpileup() 347 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); in mpileup() 397 for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); in mpileup() [all …]
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/dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/ |
H A D | bam_plcmd.c | 197 mplp_pileup_t gplp; in mpileup() local 199 memset(&gplp, 0, sizeof(mplp_pileup_t)); in mpileup() 239 gplp.n = sm->n; in mpileup() 240 gplp.n_plp = calloc(sm->n, sizeof(int)); in mpileup() 308 for (i = 0; i < gplp.n; ++i) in mpileup() 309 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); in mpileup() 316 …NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos,… in mpileup() 317 for (i = 0; i < gplp.n; ++i) in mpileup() 318 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); in mpileup() 368 for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); in mpileup() [all …]
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/dports/devel/arduino-core/Arduino-b439a77/libraries/WiFi/extras/wifi_dnld/src/SOFTWARE_FRAMEWORK/DRIVERS/PM/ |
H A D | power_clocks_lib.c | 547 void pcl_write_gplp(unsigned long gplp, unsigned long value) in pcl_write_gplp() argument 551 pm_write_gplp(&AVR32_PM,gplp,value); in pcl_write_gplp() 553 scif_write_gplp(gplp,value); in pcl_write_gplp() 557 unsigned long pcl_read_gplp(unsigned long gplp) in pcl_read_gplp() argument 561 return pm_read_gplp(&AVR32_PM,gplp); in pcl_read_gplp() 563 return scif_read_gplp(gplp); in pcl_read_gplp()
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H A D | pm.c | 510 unsigned long pm_read_gplp(volatile avr32_pm_t *pm, unsigned long gplp) in pm_read_gplp() argument 512 return pm->gplp[gplp]; in pm_read_gplp() 516 void pm_write_gplp(volatile avr32_pm_t *pm, unsigned long gplp, unsigned long value) in pm_write_gplp() argument 518 pm->gplp[gplp] = value; in pm_write_gplp()
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H A D | power_clocks_lib.h | 363 extern unsigned long pcl_read_gplp(unsigned long gplp); 371 extern void pcl_write_gplp(unsigned long gplp, unsigned long value);
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H A D | pm.h | 418 extern unsigned long pm_read_gplp(volatile avr32_pm_t *pm, unsigned long gplp); 427 extern void pm_write_gplp(volatile avr32_pm_t *pm, unsigned long gplp, unsigned long value);
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/dports/devel/arduino-core/Arduino-b439a77/hardware/arduino/avr/firmwares/wifishield/wifiHD/src/SOFTWARE_FRAMEWORK/DRIVERS/PM/ |
H A D | power_clocks_lib.c | 547 void pcl_write_gplp(unsigned long gplp, unsigned long value) in pcl_write_gplp() argument 551 pm_write_gplp(&AVR32_PM,gplp,value); in pcl_write_gplp() 553 scif_write_gplp(gplp,value); in pcl_write_gplp() 557 unsigned long pcl_read_gplp(unsigned long gplp) in pcl_read_gplp() argument 561 return pm_read_gplp(&AVR32_PM,gplp); in pcl_read_gplp() 563 return scif_read_gplp(gplp); in pcl_read_gplp()
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H A D | pm.c | 510 unsigned long pm_read_gplp(volatile avr32_pm_t *pm, unsigned long gplp) in pm_read_gplp() argument 512 return pm->gplp[gplp]; in pm_read_gplp() 516 void pm_write_gplp(volatile avr32_pm_t *pm, unsigned long gplp, unsigned long value) in pm_write_gplp() argument 518 pm->gplp[gplp] = value; in pm_write_gplp()
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H A D | power_clocks_lib.h | 363 extern unsigned long pcl_read_gplp(unsigned long gplp); 371 extern void pcl_write_gplp(unsigned long gplp, unsigned long value);
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H A D | pm.h | 418 extern unsigned long pm_read_gplp(volatile avr32_pm_t *pm, unsigned long gplp); 427 extern void pm_write_gplp(volatile avr32_pm_t *pm, unsigned long gplp, unsigned long value);
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/dports/devel/arduino-core/Arduino-b439a77/hardware/arduino/avr/firmwares/wifishield/wifi_dnld/src/SOFTWARE_FRAMEWORK/DRIVERS/PM/ |
H A D | power_clocks_lib.c | 547 void pcl_write_gplp(unsigned long gplp, unsigned long value) in pcl_write_gplp() argument 551 pm_write_gplp(&AVR32_PM,gplp,value); in pcl_write_gplp() 553 scif_write_gplp(gplp,value); in pcl_write_gplp() 557 unsigned long pcl_read_gplp(unsigned long gplp) in pcl_read_gplp() argument 561 return pm_read_gplp(&AVR32_PM,gplp); in pcl_read_gplp() 563 return scif_read_gplp(gplp); in pcl_read_gplp()
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H A D | pm.c | 510 unsigned long pm_read_gplp(volatile avr32_pm_t *pm, unsigned long gplp) in pm_read_gplp() argument 512 return pm->gplp[gplp]; in pm_read_gplp() 516 void pm_write_gplp(volatile avr32_pm_t *pm, unsigned long gplp, unsigned long value) in pm_write_gplp() argument 518 pm->gplp[gplp] = value; in pm_write_gplp()
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H A D | power_clocks_lib.h | 363 extern unsigned long pcl_read_gplp(unsigned long gplp); 371 extern void pcl_write_gplp(unsigned long gplp, unsigned long value);
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H A D | pm.h | 418 extern unsigned long pm_read_gplp(volatile avr32_pm_t *pm, unsigned long gplp); 427 extern void pm_write_gplp(volatile avr32_pm_t *pm, unsigned long gplp, unsigned long value);
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/dports/devel/arduino-core/Arduino-b439a77/libraries/WiFi/extras/wifiHD/src/SOFTWARE_FRAMEWORK/DRIVERS/PM/ |
H A D | power_clocks_lib.c | 547 void pcl_write_gplp(unsigned long gplp, unsigned long value) in pcl_write_gplp() argument 551 pm_write_gplp(&AVR32_PM,gplp,value); in pcl_write_gplp() 553 scif_write_gplp(gplp,value); in pcl_write_gplp() 557 unsigned long pcl_read_gplp(unsigned long gplp) in pcl_read_gplp() argument 561 return pm_read_gplp(&AVR32_PM,gplp); in pcl_read_gplp() 563 return scif_read_gplp(gplp); in pcl_read_gplp()
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H A D | pm.c | 510 unsigned long pm_read_gplp(volatile avr32_pm_t *pm, unsigned long gplp) in pm_read_gplp() argument 512 return pm->gplp[gplp]; in pm_read_gplp() 516 void pm_write_gplp(volatile avr32_pm_t *pm, unsigned long gplp, unsigned long value) in pm_write_gplp() argument 518 pm->gplp[gplp] = value; in pm_write_gplp()
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H A D | power_clocks_lib.h | 363 extern unsigned long pcl_read_gplp(unsigned long gplp); 371 extern void pcl_write_gplp(unsigned long gplp, unsigned long value);
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/dports/biology/seqan1/seqan-1.3.1/lib/samtools/ |
H A D | bam_plcmd.c | 627 mplp_pileup_t gplp; in mpileup() local 629 memset(&gplp, 0, sizeof(mplp_pileup_t)); in mpileup() 670 gplp.n = sm->n; in mpileup() 671 gplp.n_plp = calloc(sm->n, sizeof(int)); in mpileup() 735 for (i = 0; i < gplp.n; ++i) in mpileup() 736 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); in mpileup() 743 …if (!(conf->flag&MPLP_NO_INDEL) && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, … in mpileup() 744 for (i = 0; i < gplp.n; ++i) in mpileup() 745 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); in mpileup() 778 for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); in mpileup() [all …]
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/dports/biology/bcftools/bcftools-1.14/ |
H A D | mpileup.c | 92 mplp_pileup_t *gplp; member 563 for (i = 0; i < conf->gplp->n; ++i) in mpileup_reg() 564 … bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i); in mpileup_reg() 576 … bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref) >= 0)) in mpileup_reg() 578 for (i = 0; i < conf->gplp->n; ++i) in mpileup_reg() 579 … bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i); in mpileup_reg() 716 conf->gplp->n_plp = (int*) calloc(conf->gplp->n, sizeof(int)); in mpileup() 717 conf->gplp->m_plp = (int*) calloc(conf->gplp->n, sizeof(int)); in mpileup() 718 conf->gplp->plp = (bam_pileup1_t**) calloc(conf->gplp->n, sizeof(bam_pileup1_t*)); in mpileup() 947 for (i = 0; i < conf->gplp->n; ++i) free(conf->gplp->plp[i]); in mpileup() [all …]
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | mpileup.c | 92 mplp_pileup_t *gplp; member 563 for (i = 0; i < conf->gplp->n; ++i) in mpileup_reg() 564 … bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i); in mpileup_reg() 576 … bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref) >= 0)) in mpileup_reg() 578 for (i = 0; i < conf->gplp->n; ++i) in mpileup_reg() 579 … bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i); in mpileup_reg() 716 conf->gplp->n_plp = (int*) calloc(conf->gplp->n, sizeof(int)); in mpileup() 717 conf->gplp->m_plp = (int*) calloc(conf->gplp->n, sizeof(int)); in mpileup() 718 conf->gplp->plp = (bam_pileup1_t**) calloc(conf->gplp->n, sizeof(bam_pileup1_t*)); in mpileup() 947 for (i = 0; i < conf->gplp->n; ++i) free(conf->gplp->plp[i]); in mpileup() [all …]
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | mpileup.c | 92 mplp_pileup_t *gplp; member 563 for (i = 0; i < conf->gplp->n; ++i) in mpileup_reg() 564 … bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i); in mpileup_reg() 576 … bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref) >= 0)) in mpileup_reg() 578 for (i = 0; i < conf->gplp->n; ++i) in mpileup_reg() 579 … bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i); in mpileup_reg() 716 conf->gplp->n_plp = (int*) calloc(conf->gplp->n, sizeof(int)); in mpileup() 717 conf->gplp->m_plp = (int*) calloc(conf->gplp->n, sizeof(int)); in mpileup() 718 conf->gplp->plp = (bam_pileup1_t**) calloc(conf->gplp->n, sizeof(bam_pileup1_t*)); in mpileup() 947 for (i = 0; i < conf->gplp->n; ++i) free(conf->gplp->plp[i]); in mpileup() [all …]
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H A D | mpileup.c.pysam.c | 94 mplp_pileup_t *gplp; member 565 for (i = 0; i < conf->gplp->n; ++i) in mpileup_reg() 566 … bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i); in mpileup_reg() 578 … bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref) >= 0)) in mpileup_reg() 580 for (i = 0; i < conf->gplp->n; ++i) in mpileup_reg() 581 … bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i); in mpileup_reg() 718 conf->gplp->n_plp = (int*) calloc(conf->gplp->n, sizeof(int)); in mpileup() 719 conf->gplp->m_plp = (int*) calloc(conf->gplp->n, sizeof(int)); in mpileup() 720 conf->gplp->plp = (bam_pileup1_t**) calloc(conf->gplp->n, sizeof(bam_pileup1_t*)); in mpileup() 949 for (i = 0; i < conf->gplp->n; ++i) free(conf->gplp->plp[i]); in mpileup() [all …]
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/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | bam_plcmd.c | 499 mplp_pileup_t gplp; in mpileup() local 501 memset(&gplp, 0, sizeof(mplp_pileup_t)); in mpileup() 595 gplp.n = sm->n; in mpileup() 596 gplp.n_plp = calloc(sm->n, sizeof(int)); in mpileup() 775 for (i = 0; i < gplp.n; ++i) in mpileup() 776 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); in mpileup() 787 …NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos,… in mpileup() 790 for (i = 0; i < gplp.n; ++i) in mpileup() 791 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); in mpileup() 1065 for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); in mpileup() [all …]
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H A D | bam_plcmd.c.pysam.c | 501 mplp_pileup_t gplp; in mpileup() local 503 memset(&gplp, 0, sizeof(mplp_pileup_t)); in mpileup() 597 gplp.n = sm->n; in mpileup() 598 gplp.n_plp = calloc(sm->n, sizeof(int)); in mpileup() 777 for (i = 0; i < gplp.n; ++i) in mpileup() 778 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); in mpileup() 789 …NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos,… in mpileup() 792 for (i = 0; i < gplp.n; ++i) in mpileup() 793 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); in mpileup() 1067 for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); in mpileup() [all …]
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/dports/biology/samtools/samtools-1.14/ |
H A D | bam_plcmd.c | 499 mplp_pileup_t gplp; in mpileup() local 501 memset(&gplp, 0, sizeof(mplp_pileup_t)); in mpileup() 595 gplp.n = sm->n; in mpileup() 596 gplp.n_plp = calloc(sm->n, sizeof(int)); in mpileup() 775 for (i = 0; i < gplp.n; ++i) in mpileup() 776 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); in mpileup() 787 …NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos,… in mpileup() 790 for (i = 0; i < gplp.n; ++i) in mpileup() 791 bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); in mpileup() 1065 for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); in mpileup() [all …]
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