201 lines
7.4 KiB
C
201 lines
7.4 KiB
C
/*
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* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
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*
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* This file is part of Bowtie 2.
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*
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* Bowtie 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* Bowtie 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#ifndef OPTS_H_
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#define OPTS_H_
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enum {
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ARG_ORIG = 256, // --orig
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ARG_SEED, // --seed
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ARG_SOLEXA_QUALS, // --solexa-quals
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ARG_VERBOSE, // --verbose
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ARG_STARTVERBOSE, // --startverbose
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ARG_QUIET, // --quiet
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ARG_METRIC_IVAL, // --met
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ARG_METRIC_FILE, // --met-file
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ARG_METRIC_STDERR, // --met-stderr
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ARG_METRIC_PER_READ, // --met-per-read
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ARG_REFIDX, // --refidx
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ARG_SANITY, // --sanity
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ARG_PARTITION, // --partition
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ARG_INTEGER_QUALS, // --int-quals
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ARG_FILEPAR, // --filepar
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ARG_SHMEM, // --shmem
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ARG_MM, // --mm
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ARG_MMSWEEP, // --mmsweep
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ARG_FF, // --ff
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ARG_FR, // --fr
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ARG_RF, // --rf
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ARG_NO_MIXED, // --no-mixed
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ARG_NO_DISCORDANT, // --no-discordant
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ARG_CACHE_LIM, // --
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ARG_CACHE_SZ, // --
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ARG_NO_FW, // --nofw
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ARG_NO_RC, // --norc
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ARG_SKIP, // --skip
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ARG_ONETWO, // --12
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ARG_PHRED64, // --phred64
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ARG_PHRED33, // --phred33
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ARG_HADOOPOUT, // --hadoopout
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ARG_FUZZY, // --fuzzy
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ARG_FULLREF, // --fullref
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ARG_USAGE, // --usage
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ARG_SNPPHRED, // --snpphred
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ARG_SNPFRAC, // --snpfrac
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ARG_SAM_NO_QNAME_TRUNC, // --sam-no-qname-trunc
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ARG_SAM_OMIT_SEC_SEQ, // --sam-omit-sec-seq
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ARG_SAM_NOHEAD, // --sam-noHD/--sam-nohead
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ARG_SAM_NOSQ, // --sam-nosq/--sam-noSQ
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ARG_SAM_RG, // --sam-rg
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ARG_SAM_RGID, // --sam-rg-id
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ARG_GAP_BAR, // --gbar
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ARG_QUALS1, // --Q1
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ARG_QUALS2, // --Q2
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ARG_QSEQ, // --qseq
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ARG_SEED_SUMM, // --seed-summary
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ARG_OVERHANG, // --overhang
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ARG_NO_CACHE, // --no-cache
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ARG_USE_CACHE, // --cache
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ARG_NOISY_HPOLY, // --454/--ion-torrent
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ARG_LOCAL, // --local
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ARG_END_TO_END, // --end-to-end
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ARG_SCAN_NARROWED, // --scan-narrowed
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ARG_QC_FILTER, // --qc-filter
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ARG_BWA_SW_LIKE, // --bwa-sw-like
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ARG_MULTISEED_IVAL, // --multiseed
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ARG_SCORE_MIN, // --score-min
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ARG_SCORE_MA, // --ma
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ARG_SCORE_MMP, // --mp
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ARG_SCORE_SCP, // --sp
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ARG_NO_SOFTCLIP, // --no-softclip
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ARG_SCORE_NP, // --nm
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ARG_SCORE_RDG, // --rdg
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ARG_SCORE_RFG, // --rfg
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ARG_N_CEIL, // --n-ceil
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ARG_DPAD, // --dpad
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ARG_SAM_PRINT_YI, // --mapq-print-inputs
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ARG_ALIGN_POLICY, // --policy
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ARG_PRESET_VERY_FAST, // --very-fast
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ARG_PRESET_FAST, // --fast
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ARG_PRESET_SENSITIVE, // --sensitive
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ARG_PRESET_VERY_SENSITIVE, // --very-sensitive
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ARG_PRESET_VERY_FAST_LOCAL, // --very-fast-local
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ARG_PRESET_FAST_LOCAL, // --fast-local
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ARG_PRESET_SENSITIVE_LOCAL, // --sensitive-local
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ARG_PRESET_VERY_SENSITIVE_LOCAL, // --very-sensitive-local
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ARG_NO_SCORE_PRIORITY, // --no-score-priority
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ARG_IGNORE_QUALS, // --ignore-quals
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ARG_DESC, // --arg-desc
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ARG_TAB5, // --tab5
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ARG_TAB6, // --tab6
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ARG_WRAPPER, // --wrapper
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ARG_DOVETAIL, // --dovetail
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ARG_NO_DOVETAIL, // --no-dovetail
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ARG_CONTAIN, // --contain
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ARG_NO_CONTAIN, // --no-contain
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ARG_OVERLAP, // --overlap
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ARG_NO_OVERLAP, // --no-overlap
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ARG_MAPQ_V, // --mapq-v
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ARG_SSE8, // --sse8
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ARG_SSE8_NO, // --no-sse8
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ARG_UNGAPPED, // --ungapped
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ARG_UNGAPPED_NO, // --no-ungapped
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ARG_TIGHTEN, // --tighten
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ARG_UNGAP_THRESH, // --ungap-thresh
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ARG_EXACT_UPFRONT, // --exact-upfront
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ARG_1MM_UPFRONT, // --1mm-upfront
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ARG_EXACT_UPFRONT_NO, // --no-exact-upfront
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ARG_1MM_UPFRONT_NO, // --no-1mm-upfront
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ARG_1MM_MINLEN, // --1mm-minlen
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ARG_VERSION, // --version
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ARG_SEED_OFF, // --seed-off
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ARG_SEED_BOOST_THRESH, // --seed-boost
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ARG_MAX_SEEDS,
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ARG_READ_TIMES, // --read-times
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ARG_EXTEND_ITERS, // --extends
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ARG_DP_MATE_STREAK_THRESH, // --db-mate-streak
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ARG_DP_FAIL_STREAK_THRESH, // --dp-fail-streak
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ARG_UG_FAIL_STREAK_THRESH, // --ug-fail-streak
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ARG_EE_FAIL_STREAK_THRESH, // --ee-fail-streak
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ARG_DP_FAIL_THRESH, // --dp-fails
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ARG_UG_FAIL_THRESH, // --ug-fails
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ARG_MAPQ_EX, // --mapq-extra
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ARG_NO_EXTEND, // --no-extend
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ARG_REORDER, // --reorder
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ARG_SHOW_RAND_SEED, // --show-rand-seed
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ARG_READ_PASSTHRU, // --passthrough
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ARG_SAMPLE, // --sample
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ARG_CP_MIN, // --cp-min
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ARG_CP_IVAL, // --cp-ival
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ARG_TRI, // --tri
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ARG_LOCAL_SEED_CACHE_SZ, // --local-seed-cache-sz
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ARG_CURRENT_SEED_CACHE_SZ, // --seed-cache-sz
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ARG_SAM_NO_UNAL, // --no-unal
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ARG_NON_DETERMINISTIC, // --non-deterministic
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ARG_TEST_25, // --test-25
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ARG_DESC_KB, // --desc-kb
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ARG_DESC_LANDING, // --desc-landing
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ARG_DESC_EXP, // --desc-exp
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ARG_DESC_FMOPS, // --desc-fmops
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ARG_NO_TEMPSPLICESITE,
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ARG_PEN_CANSPLICE,
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ARG_PEN_NONCANSPLICE,
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ARG_PEN_CONFLICTSPLICE,
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ARG_PEN_CANINTRONLEN,
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ARG_PEN_NONCANINTRONLEN,
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ARG_MIN_INTRONLEN,
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ARG_MAX_INTRONLEN,
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ARG_KNOWN_SPLICESITE_INFILE,
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ARG_NOVEL_SPLICESITE_INFILE,
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ARG_NOVEL_SPLICESITE_OUTFILE,
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ARG_SECONDARY,
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ARG_NO_SPLICED_ALIGNMENT,
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ARG_RNA_STRANDNESS,
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ARG_SPLICESITE_DB_ONLY,
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ARG_NO_ANCHORSTOP,
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ARG_TRANSCRIPTOME_MAPPING_ONLY,
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ARG_TRANSCRIPTOME_ASSEMBLY,
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ARG_TRANSCRIPTOME_ASSEMBLY_CUFFLINKS,
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ARG_AVOID_PSEUDOGENE,
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#ifdef USE_SRA
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ARG_SRA_ACC,
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#endif
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ARG_REMOVE_CHRNAME,
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ARG_ADD_CHRNAME,
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ARG_MAX_ALTSTRIED,
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ARG_HAPLOTYPE,
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ARG_CODIS,
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ARG_NO_TEMPLATELEN_ADJUSTMENT,
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ARG_SUMMARY_FILE,
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ARG_NEW_SUMMARY,
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ARG_DP,
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ARG_REPEAT,
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ARG_NO_REPEAT_INDEX,
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ARG_READ_LENGTHS,
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ARG_BASE_CHANGE, // --base-change
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ARG_REPEAT_LIMIT,
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ARG_UNIQUE_ONLY,
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ARG_3N,
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ARG_DIRECTIONAL,
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ARG_DIRECTIONAL_REVERSE
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};
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#endif
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