1010#include "kseq.h"
1111
1212const char PROG [20 ] = "TideHunter" ;
13- const char VERSION [20 ] = "1.4.2 " ;
13+ const char VERSION [20 ] = "1.4.3 " ;
1414const char CONTACT [30 ] = "yangao07@hit.edu.cn" ;
1515
1616const struct option mini_tandem_opt [] = {
@@ -76,22 +76,22 @@ static int usage(void)
7676
7777 err_printf ("Options: \n" );
7878 err_printf (" Seeding:\n" );
79- err_printf (" -k --kmer-length INT k-mer length (no larger than %d). [%d]\n" , MAX_KMER_SIZE , KMER_SIZE );
80- err_printf (" -w --window-size INT window size. [%d]\n" , KMER_WSIZE );
81- err_printf (" -s --step-size INT step size. [%d]\n" , KMER_SSIZE );
82- //err_printf(" -m --minimal-m [INT] number of minimal k-mer to keep in each window. [%d]\n", KMER_MINM);
83- err_printf (" -H --HPC-kmer use homopolymer-compressed k-mer. [False]\n" );
79+ err_printf (" -k --kmer-length INT k-mer length (no larger than %d) [%d]\n" , MAX_KMER_SIZE , KMER_SIZE );
80+ err_printf (" -w --window-size INT window size [%d]\n" , KMER_WSIZE );
81+ err_printf (" -s --step-size INT step size [%d]\n" , KMER_SSIZE );
82+ //err_printf(" -m --minimal-m [INT] number of minimal k-mer to keep in each window [%d]\n", KMER_MINM);
83+ err_printf (" -H --HPC-kmer use homopolymer-compressed k-mer [False]\n" );
8484
8585 //err_printf("\n");
8686
8787 err_printf (" Tandem repeat criteria:\n" );
8888 // TODO min_copy < 2 ???
89- err_printf (" -c --min-copy INT minimum copy number of tandem repeat. [%d]\n" , MIN_COPY );
90- err_printf (" -e --max-diverg INT maximum allowed divergence rate between two consecutive repeats. [%.2f]\n" , MAX_DIV );
91- err_printf (" -p --min-period INT minimum period size of tandem repeat. (>=%u) [%u]\n" , MIN_PERIOD , DEF_MIN_PERIOD );
92- err_printf (" -P --max-period INT maximum period size of tandem repeat. (<=%u) [%s]\n" , MAX_PERIOD , DEF_MAX_PERIOD_STR );
89+ err_printf (" -c --min-copy INT minimum copy number of tandem repeat [%d]\n" , MIN_COPY );
90+ err_printf (" -e --max-diverg INT maximum allowed divergence rate between two consecutive repeats [%.2f]\n" , MAX_DIV );
91+ err_printf (" -p --min-period INT minimum period size of tandem repeat (>=%u) [%u]\n" , MIN_PERIOD , DEF_MIN_PERIOD );
92+ err_printf (" -P --max-period INT maximum period size of tandem repeat (<=%u) [%s]\n" , MAX_PERIOD , DEF_MAX_PERIOD_STR );
9393
94- // err_printf(" -r --rep-range [INT] maximum range to find tandem repeat. [%d]\n", REP_RANGE);
94+ // err_printf(" -r --rep-range [INT] maximum range to find tandem repeat [%d]\n", REP_RANGE);
9595// err_printf(" (-1: no limit, tandem repeat can span the whole sequence)\n");
9696 //err_printf("\n");
9797
@@ -105,32 +105,32 @@ static int usage(void)
105105 err_printf (" - affine (set O2 as 0): O1+g*E1\n" );
106106 err_printf (" - linear (set O1 as 0): g*E1\n" );
107107 err_printf (" Adapter sequence:\n" );
108- err_printf (" -5 --five-prime STR 5' adapter sequence (sense strand). [NULL]\n" );
109- err_printf (" -3 --three-prime STR 3' adapter sequence (anti-sense strand). [NULL]\n" );
110- err_printf (" -a --ada-mat-rat FLT minimum match ratio of adapter sequence. [%.2f]\n" , ADA_MATCH_RAT );
108+ err_printf (" -5 --five-prime STR 5' adapter sequence (sense strand) [NULL]\n" );
109+ err_printf (" -3 --three-prime STR 3' adapter sequence (anti-sense strand) [NULL]\n" );
110+ err_printf (" -a --ada-mat-rat FLT minimum match ratio of adapter sequence [%.2f]\n" , ADA_MATCH_RAT );
111111
112112 //err_printf("\n");
113113
114114 err_printf (" Output:\n" );
115- err_printf (" -o --output STR output file. [stdout]\n" );
116- err_printf (" -u --unit-seq only output the unit sequences of each tandem repeat, no consensus sequence. [False]\n" );
117- err_printf (" -l --longest only output the consensus sequence of the tandem repeat that covers the longest read sequence. [False]\n" );
118- err_printf (" -F --full-len only output full-length consensus sequence. [False]\n" );
119- err_printf (" -f --out-fmt INT output format. [%d]\n" , FASTA_FMT );
115+ err_printf (" -o --output STR output file [stdout]\n" );
116+ err_printf (" -u --unit-seq only output the unit sequences of each tandem repeat, no consensus sequence [False]\n" );
117+ err_printf (" -l --longest only output the consensus sequence of the tandem repeat that covers the longest read sequence [False]\n" );
118+ err_printf (" -F --full-len only output full-length consensus sequence [False]\n" );
119+ err_printf (" -f --out-fmt INT output format [%d]\n" , FASTA_FMT );
120120 err_printf (" - %d: FASTA\n" , FASTA_FMT );
121121 err_printf (" - %d: Tabular\n" , TAB_FMT );
122- //err_printf(" -S --splint-seq STR splint sequence in FASTA/FASTQ format. [NULL]\n");
123- //err_printf(" -d --detail-out STR detailed information of each consensus. [NULL]\n");
122+ //err_printf(" -S --splint-seq STR splint sequence in FASTA/FASTQ format [NULL]\n");
123+ //err_printf(" -d --detail-out STR detailed information of each consensus [NULL]\n");
124124 //err_printf(" (start, end, score, etc.)\n");
125125
126126 //err_printf("\n");
127127
128128 err_printf (" Computing resource:\n" );
129- err_printf (" -t --thread INT number of threads to use. [%d]\n\n" , THREAD_N );
129+ err_printf (" -t --thread INT number of threads to use [%d]\n\n" , THREAD_N );
130130
131131 err_printf (" General options:\n" );
132- err_printf (" -h --help print this help usage information. \n" );
133- err_printf (" -v --version show version number. \n" );
132+ err_printf (" -h --help print this help usage information\n" );
133+ err_printf (" -v --version show version number\n" );
134134
135135 err_printf ("\n" );
136136 return 1 ;
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