/
opts.h
147 lines (147 loc) · 2.4 KB
/
opts.h
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#ifndef OPTS_H_
#define OPTS_H_
enum
{
ARG_ORIG = 256,
ARG_SEED,
ARG_SOLEXA_QUALS,
ARG_VERBOSE,
ARG_STARTVERBOSE,
ARG_QUIET,
ARG_METRIC_IVAL,
ARG_METRIC_FILE,
ARG_METRIC_STDERR,
ARG_METRIC_PER_READ,
ARG_REFIDX,
ARG_SANITY,
ARG_PARTITION,
ARG_INTEGER_QUALS,
ARG_FILEPAR,
ARG_READS_PER_BATCH,
ARG_SHMEM,
ARG_MM,
ARG_MMSWEEP,
ARG_FF,
ARG_FR,
ARG_RF,
ARG_NO_MIXED,
ARG_NO_DISCORDANT,
ARG_CACHE_LIM,
ARG_CACHE_SZ,
ARG_NO_FW,
ARG_NO_RC,
ARG_SKIP,
ARG_ONETWO,
ARG_PHRED64,
ARG_PHRED33,
ARG_HADOOPOUT,
ARG_FULLREF,
ARG_USAGE,
ARG_SNPPHRED,
ARG_SNPFRAC,
ARG_SAM_NO_QNAME_TRUNC,
ARG_SAM_OMIT_SEC_SEQ,
ARG_SAM_NOHEAD,
ARG_SAM_NOSQ,
ARG_SAM_RG,
ARG_SAM_RGID,
ARG_GAP_BAR,
ARG_QUALS1,
ARG_QUALS2,
ARG_QSEQ,
ARG_SEED_SUMM,
ARG_SC_UNMAPPED,
ARG_OVERHANG,
ARG_NO_CACHE,
ARG_USE_CACHE,
ARG_NOISY_HPOLY,
ARG_LOCAL,
ARG_END_TO_END,
ARG_SCAN_NARROWED,
ARG_QC_FILTER,
ARG_BWA_SW_LIKE,
ARG_MULTISEED_IVAL,
ARG_SCORE_MIN,
ARG_SCORE_MA,
ARG_SCORE_MMP,
ARG_SCORE_NP,
ARG_SCORE_RDG,
ARG_SCORE_RFG,
ARG_N_CEIL,
ARG_DPAD,
ARG_SAM_PRINT_YI,
ARG_ALIGN_POLICY,
ARG_PRESET_VERY_FAST,
ARG_PRESET_FAST,
ARG_PRESET_SENSITIVE,
ARG_PRESET_VERY_SENSITIVE,
ARG_PRESET_VERY_FAST_LOCAL,
ARG_PRESET_FAST_LOCAL,
ARG_PRESET_SENSITIVE_LOCAL,
ARG_PRESET_VERY_SENSITIVE_LOCAL,
ARG_IGNORE_QUALS,
ARG_DESC,
ARG_TAB5,
ARG_TAB6,
ARG_WRAPPER,
ARG_DOVETAIL,
ARG_NO_DOVETAIL,
ARG_CONTAIN,
ARG_NO_CONTAIN,
ARG_OVERLAP,
ARG_NO_OVERLAP,
ARG_MAPQ_V,
ARG_SSE8,
ARG_SSE8_NO,
ARG_UNGAPPED,
ARG_UNGAPPED_NO,
ARG_TIGHTEN,
ARG_UNGAP_THRESH,
ARG_EXACT_UPFRONT,
ARG_1MM_UPFRONT,
ARG_EXACT_UPFRONT_NO,
ARG_1MM_UPFRONT_NO,
ARG_1MM_MINLEN,
ARG_VERSION,
ARG_SEED_OFF,
ARG_SEED_BOOST_THRESH,
ARG_READ_TIMES,
ARG_EXTEND_ITERS,
ARG_DP_MATE_STREAK_THRESH,
ARG_DP_FAIL_STREAK_THRESH,
ARG_UG_FAIL_STREAK_THRESH,
ARG_EE_FAIL_STREAK_THRESH,
ARG_DP_FAIL_THRESH,
ARG_UG_FAIL_THRESH,
ARG_MAPQ_EX,
ARG_NO_EXTEND,
ARG_REORDER,
ARG_SHOW_RAND_SEED,
ARG_READ_PASSTHRU,
ARG_SAMPLE,
ARG_CP_MIN,
ARG_CP_IVAL,
ARG_TRI,
ARG_LOCAL_SEED_CACHE_SZ,
ARG_CURRENT_SEED_CACHE_SZ,
ARG_SAM_NO_UNAL,
ARG_NON_DETERMINISTIC,
ARG_TEST_25,
ARG_DESC_KB,
ARG_DESC_LANDING,
ARG_DESC_EXP,
ARG_DESC_PRIORITIZE,
ARG_DESC_FMOPS,
ARG_LOG_DP,
ARG_LOG_DP_OPP,
ARG_XEQ,
ARG_THREAD_CEILING,
ARG_THREAD_PIDDIR,
ARG_INTERLEAVED,
ARG_TRIM_TO,
ARG_PRESERVE_TAGS,
ARG_ALIGN_PAIRED_READS,
ARG_SRA_ACC,
ARG_SAM_APPEND_COMMENT,
};
#endif