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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| /* bam_sample.c -- group data by sample. | ||
| Copyright (C) 2010, 2011 Broad Institute. | ||
| Copyright (C) 2013, 2016-2018 Genome Research Ltd. | ||
| Copyright (C) 2013, 2016-2022 Genome Research Ltd. | ||
| Author: Heng Li <[email protected]>, Petr Danecek <[email protected]> | ||
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@@ -281,7 +281,7 @@ int bam_smpl_add_samples(bam_smpl_t *bsmpl, char *list, int is_file) | |
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| int i, nsamples = 0; | ||
| char **samples = hts_readlist(list, is_file, &nsamples); | ||
| if ( !nsamples ) return 0; | ||
| if ( !samples || !nsamples ) return 0; | ||
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| kstring_t ori = {0,0,0}; | ||
| kstring_t ren = {0,0,0}; | ||
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@@ -328,7 +328,7 @@ int bam_smpl_add_readgroups(bam_smpl_t *bsmpl, char *list, int is_file) | |
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| int i, nrows = 0; | ||
| char **rows = hts_readlist(list, is_file, &nrows); | ||
| if ( !nrows ) return 0; | ||
| if ( !rows || !nrows ) return 0; | ||
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| kstring_t fld1 = {0,0,0}; | ||
| kstring_t fld2 = {0,0,0}; | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| /* bcftools.h -- utility function declarations. | ||
| Copyright (C) 2013-2021 Genome Research Ltd. | ||
| Copyright (C) 2013-2022 Genome Research Ltd. | ||
| Author: Petr Danecek <[email protected]> | ||
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@@ -28,6 +28,7 @@ THE SOFTWARE. */ | |
| #include <stdarg.h> | ||
| #include <htslib/hts_defs.h> | ||
| #include <htslib/vcf.h> | ||
| #include <htslib/synced_bcf_reader.h> | ||
| #include <math.h> | ||
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| #define FT_TAB_TEXT 0 // custom tab-delimited text file | ||
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@@ -50,9 +51,11 @@ void error_errno(const char *format, ...) HTS_NORETURN HTS_FORMAT(HTS_PRINTF_FMT | |
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| void bcf_hdr_append_version(bcf_hdr_t *hdr, int argc, char **argv, const char *cmd); | ||
| const char *hts_bcf_wmode(int file_type); | ||
| const char *hts_bcf_wmode2(int file_type, char *fname); | ||
| void set_wmode(char dst[8], int file_type, char *fname, int compression_level); // clevel: 0-9 with or zb type, -1 unset | ||
| const char *hts_bcf_wmode2(int file_type, const char *fname); | ||
| void set_wmode(char dst[8], int file_type, const char *fname, int compression_level); // clevel: 0-9 with or zb type, -1 unset | ||
| char *init_tmp_prefix(const char *prefix); | ||
| int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq); | ||
| int parse_overlap_option(const char *arg); | ||
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| void *smalloc(size_t size); // safe malloc | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| /* The MIT License | ||
| Copyright (c) 2016 Genome Research Ltd. | ||
| Copyright (c) 2016-2022 Genome Research Ltd. | ||
| Author: Petr Danecek <[email protected]> | ||
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@@ -43,6 +43,7 @@ bin_t *bin_init(const char *list_def, float min, float max) | |
| int is_file = strchr(list_def,',') ? 0 : 1; | ||
| int i, nlist; | ||
| char **list = hts_readlist(list_def, is_file, &nlist); | ||
| if ( !list ) error("Error: failed to read %s\n",list_def); | ||
| bin->nbins = nlist; | ||
| bin->bins = (float*) malloc(sizeof(float)*nlist); | ||
| for (i=0; i<nlist; i++) | ||
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