Searched refs:use_seqid (Results 1 – 2 of 2) sorted by relevance
| /dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-pileup/ |
| H A D | sam-hdr1.c | 465 static rc_t collect_from_references( headers * h, int hdr_idx, input_files * ifs , bool use_seqid) in collect_from_references() argument
499 … string_printf( buffer, sizeof buffer, &num_writ, "@SQ\tSN:%s\tLN:%lu", use_seqid?seqid:name, seq_… in collect_from_references()
731 static rc_t collect_from_bam_hdr( headers * dst, input_files * ifs, bool use_seqid ) in collect_from_bam_hdr() argument
738 if ( rc == 0 && ( count == 0 || use_seqid ) ) in collect_from_bam_hdr()
739 rc = collect_from_references( dst, 2, ifs , use_seqid); in collect_from_bam_hdr()
751 static rc_t collect_by_recalc( headers * h, input_files * ifs, bool use_seqid ) in collect_by_recalc() argument
753 rc_t rc = collect_from_references( h, 1, ifs, use_seqid ); in collect_by_recalc()
760 …collect_from_src_and_files( headers * h, input_files * ifs, const char * filename, bool use_seqid ) in collect_from_src_and_files() argument
762 rc_t rc = collect_from_bam_hdr( h, ifs, use_seqid ); in collect_from_src_and_files()
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| H A D | sam-dump.c | 122 bool use_seqid; member
402 if ( param->use_seqid && seqid != NULL && seqid[ 0 ] != '\0' ) in RefSeqPrint()
620 if ( param->use_seqid ) in Cache_Unpack()
1354 if ( param->use_seqid ) in DumpAlignedFastX()
1531 if ( param->use_seqid ) in DumpAlignedSAM()
1807 int c = param->use_seqid ? alg_REF_SEQ_ID : alg_REF_NAME; in DumpUnalignedReads()
3549 if ( param->use_seqid ) in SetupColumns()
4723 parms.use_seqid = ( ( count[ earg_seq_id ] != 0 ) || multipass ); in GetArgs()
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