| /dports/biology/iolib/io_lib-io_lib-1-14-10/io_lib/ |
| H A D | scram.c | 149 if (!fd->is_bam) in scram_input_bam_block()
214 fd->is_bam = 0; in scram_open()
220 fd->is_bam = 1; in scram_open()
236 fd->is_bam = 0; in scram_open()
245 fd->is_bam = 1; in scram_open()
281 fd->is_bam = 0; in scram_open_cram_via_callbacks()
320 if (fd->is_bam) in scram_set_refs()
388 if (fd->is_bam) in scram_set_option()
409 return fd->is_bam in scram_set_option()
415 return fd->is_bam in scram_set_option()
[all …]
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| H A D | scram.h | 57 int is_bam; member
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| /dports/biology/bwa/bwa-0.7.17/bwakit/ |
| H A D | run-bwamem | 110 my $is_bam = $ARGV[1] =~ /\.bam$/? 1 : 0;
118 if ($is_bam && !defined($opts{R})) {
134 if ($is_bam) {
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| /dports/multimedia/v4l_compat/linux-5.13-rc2/drivers/mtd/nand/raw/ |
| H A D | qcom_nandc.c | 482 bool is_bam; member
538 if (!nandc->props->is_bam) in clear_bam_transaction()
1035 if (nandc->props->is_bam) in read_reg_dma()
1079 if (nandc->props->is_bam) in write_reg_dma()
1102 if (nandc->props->is_bam) in read_data_dma()
1120 if (nandc->props->is_bam) in write_data_dma()
1157 if (nandc->props->is_bam) in config_nand_cw_read()
3120 .is_bam = false,
3126 .is_bam = true,
3133 .is_bam = true,
[all …]
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| /dports/multimedia/v4l-utils/linux-5.13-rc2/drivers/mtd/nand/raw/ |
| H A D | qcom_nandc.c | 482 bool is_bam; member
538 if (!nandc->props->is_bam) in clear_bam_transaction()
1035 if (nandc->props->is_bam) in read_reg_dma()
1079 if (nandc->props->is_bam) in write_reg_dma()
1102 if (nandc->props->is_bam) in read_data_dma()
1120 if (nandc->props->is_bam) in write_data_dma()
1157 if (nandc->props->is_bam) in config_nand_cw_read()
3120 .is_bam = false,
3126 .is_bam = true,
3133 .is_bam = true,
[all …]
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| /dports/multimedia/libv4l/linux-5.13-rc2/drivers/mtd/nand/raw/ |
| H A D | qcom_nandc.c | 482 bool is_bam; member
538 if (!nandc->props->is_bam) in clear_bam_transaction()
1035 if (nandc->props->is_bam) in read_reg_dma()
1079 if (nandc->props->is_bam) in write_reg_dma()
1102 if (nandc->props->is_bam) in read_data_dma()
1120 if (nandc->props->is_bam) in write_data_dma()
1157 if (nandc->props->is_bam) in config_nand_cw_read()
3120 .is_bam = false,
3126 .is_bam = true,
3133 .is_bam = true,
[all …]
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| /dports/biology/py-deeptools/deepTools-3.5.1/deeptools/ |
| H A D | bamHandler.py | 86 elif bam.is_bam:
94 if bam.is_bam or (bam.is_cram and returnStats):
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| /dports/biology/bwa/bwa-0.7.17/ |
| H A D | bwaseqio.c | 19 int is_bam, which; // 1st bit: read1, 2nd bit: read2, 3rd: SE member
30 bs->is_bam = 1; in bwa_bam_open()
52 if (bs->is_bam) { in bwa_seq_close()
162 …if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); // l_bc has no effect fo… in bwa_read_seq()
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| /dports/biology/subread/subread-2.0.2-source/src/ |
| H A D | coverage_calc.c | 392 int is_bam = is_certainly_bam_file(input_file_name, NULL, NULL); in main() local
394 if(1==is_bam) is_BAM_input = 1; in main()
395 else if(is_bam < 0) in main()
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| H A D | propmapped.c | 516 int is_bam = is_certainly_bam_file(context -> input_file_name, NULL, NULL); in main() local
518 if(1==is_bam){ in main()
521 else if(is_bam < 0) in main()
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| H A D | core.c | 923 int convert_BAM_to_SAM(global_context_t * global_context, char * fname, int is_bam) argument
938 sambam_reader = SamBam_fopen(fname, is_bam?SAMBAM_FILE_BAM:SAMBAM_FILE_SAM);
974 …print_in_box(80,0,0,"The input %s file contains %s-end reads.", is_bam?"BAM":"SAM", global_contex…
976 print_in_box(80,0,0,"The input %s file is unsorted. Reorder it...", is_bam?"BAM":"SAM");
977 else if(is_bam)
981 if(is_bam || (global_context->input_reads.is_paired_end_reads && !is_file_sorted))
984 sambam_reader = SamBam_fopen(fname, is_bam?SAMBAM_FILE_BAM: SAMBAM_FILE_SAM);
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| H A D | sambam-file.c | 94 int is_bam = (h2[0]==31) && (h2[1]==139); in is_paired_end_BAM() local
99 sambam_reader = SamBam_fopen(fn, is_bam?SAMBAM_FILE_BAM:SAMBAM_FILE_SAM); in is_paired_end_BAM()
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| /dports/biology/iolib/io_lib-io_lib-1-14-10/progs/ |
| H A D | scram_test.c | 206 if (!in->is_bam && ref_fn) in main()
225 if (in->is_bam) { in main()
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| H A D | scram_flagstat.c | 206 if (!in->is_bam && ref_fn) in main()
229 if (in->is_bam) { in main()
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| H A D | scramble.c | 393 if (!in->is_bam && ref_fn) { in main()
572 if (in->is_bam) { in main()
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| H A D | scram_merge.c | 267 if (in[i]->is_bam) { in main()
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| /dports/biology/py-pysam/pysam-0.18.0/pysam/ |
| H A D | libcalignmentfile.pyx | 778 if not self.is_bam and not self.is_cram:
964 if self.is_bam or self.is_cram:
1005 if self.is_bam or self.is_cram:
1099 if self.is_bam or self.is_cram:
1849 if not self.is_bam and self.header.nreferences == 0:
2911 assert samfile.is_bam, "can only apply IndexReads on bam files"
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| H A D | libchtslib.pyx | 451 def is_bam(self): member in HTSFile
|