Home
last modified time | relevance | path

Searched refs:gplp (Results 1 – 25 of 37) sorted by relevance

12

/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/
H A Dbam_plcmd.c218 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 …]
/dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/
H A Dbam_plcmd.c197 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 …]
/dports/devel/arduino-core/Arduino-b439a77/libraries/WiFi/extras/wifi_dnld/src/SOFTWARE_FRAMEWORK/DRIVERS/PM/
H A Dpower_clocks_lib.c547 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()
H A Dpm.c510 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()
H A Dpower_clocks_lib.h363 extern unsigned long pcl_read_gplp(unsigned long gplp);
371 extern void pcl_write_gplp(unsigned long gplp, unsigned long value);
H A Dpm.h418 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);
/dports/devel/arduino-core/Arduino-b439a77/hardware/arduino/avr/firmwares/wifishield/wifiHD/src/SOFTWARE_FRAMEWORK/DRIVERS/PM/
H A Dpower_clocks_lib.c547 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()
H A Dpm.c510 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()
H A Dpower_clocks_lib.h363 extern unsigned long pcl_read_gplp(unsigned long gplp);
371 extern void pcl_write_gplp(unsigned long gplp, unsigned long value);
H A Dpm.h418 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);
/dports/devel/arduino-core/Arduino-b439a77/hardware/arduino/avr/firmwares/wifishield/wifi_dnld/src/SOFTWARE_FRAMEWORK/DRIVERS/PM/
H A Dpower_clocks_lib.c547 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()
H A Dpm.c510 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()
H A Dpower_clocks_lib.h363 extern unsigned long pcl_read_gplp(unsigned long gplp);
371 extern void pcl_write_gplp(unsigned long gplp, unsigned long value);
H A Dpm.h418 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);
/dports/devel/arduino-core/Arduino-b439a77/libraries/WiFi/extras/wifiHD/src/SOFTWARE_FRAMEWORK/DRIVERS/PM/
H A Dpower_clocks_lib.c547 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()
H A Dpm.c510 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()
H A Dpower_clocks_lib.h363 extern unsigned long pcl_read_gplp(unsigned long gplp);
371 extern void pcl_write_gplp(unsigned long gplp, unsigned long value);
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/
H A Dbam_plcmd.c627 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 …]
/dports/biology/bcftools/bcftools-1.14/
H A Dmpileup.c92 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 …]
/dports/biology/bio-mocha/bcftools-1.14/
H A Dmpileup.c92 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 …]
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dmpileup.c92 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 …]
H A Dmpileup.c.pysam.c94 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 …]
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam_plcmd.c499 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 …]
H A Dbam_plcmd.c.pysam.c501 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 …]
/dports/biology/samtools/samtools-1.14/
H A Dbam_plcmd.c499 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 …]

12