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Add '-E max_len' to 'seqtk seq' #148

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Add '-E max_len' to 'seqtk seq' #148

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2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
CC=gcc
CFLAGS=-g -Wall -O2 -Wno-unused-function
CFLAGS=-g -Wall -Ofast -Wno-unused-function
BINDIR=/usr/local/bin

all:seqtk
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9 changes: 6 additions & 3 deletions seqtk.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1215,14 +1215,14 @@ int stk_seq(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq;
int c, qual_thres = 0, flag = 0, qual_shift = 33, mask_chr = 0, min_len = 0, max_q = 255, fake_qual = -1;
int c, qual_thres = 0, flag = 0, qual_shift = 33, mask_chr = 0, min_len = 0, max_len = INT_MAX, max_q = 255, fake_qual = -1;
unsigned i, line_len = 0;
int64_t n_seqs = 0;
double frac = 1.;
khash_t(reg) *h = 0;
krand_t *kr = 0;

while ((c = getopt(argc, argv, "N12q:l:Q:aACrn:s:f:M:L:cVUX:SF:")) >= 0) {
while ((c = getopt(argc, argv, "N12q:l:Q:aACrn:s:f:M:L:E:cVUX:SF:")) >= 0) {
switch (c) {
case 'a':
case 'A': flag |= 1; break;
Expand All @@ -1242,6 +1242,7 @@ int stk_seq(int argc, char *argv[])
case 'X': max_q = atoi(optarg); break;
case 'l': line_len = atoi(optarg); break;
case 'L': min_len = atoi(optarg); break;
case 'E': max_len = atoi(optarg); break;
case 's': kr = kr_srand(atol(optarg)); break;
case 'f': frac = atof(optarg); break;
case 'F': fake_qual = *optarg; break;
Expand All @@ -1259,7 +1260,8 @@ int stk_seq(int argc, char *argv[])
fprintf(stderr, " -s INT random seed (effective with -f) [11]\n");
fprintf(stderr, " -f FLOAT sample FLOAT fraction of sequences [1]\n");
fprintf(stderr, " -M FILE mask regions in BED or name list FILE [null]\n");
fprintf(stderr, " -L INT drop sequences with length shorter than INT [0]\n");
fprintf(stderr, " -L INT drop sequences with length shorter than INT [%d]\n", min_len);
fprintf(stderr, " -E INT drop sequences with length longer than INT [%d]\n", max_len);
fprintf(stderr, " -F CHAR fake FASTQ quality []\n");
fprintf(stderr, " -c mask complement region (effective with -M)\n");
fprintf(stderr, " -r reverse complement\n");
Expand All @@ -1286,6 +1288,7 @@ int stk_seq(int argc, char *argv[])
while (kseq_read(seq) >= 0) {
++n_seqs;
if (seq->seq.l < min_len) continue; // NB: length filter before taking random
if (seq->seq.l > max_len) continue; // NB: length filter before taking random
if (frac < 1. && kr_drand(kr) >= frac) continue;
if (flag & 48) { // then choose odd/even reads only
if ((flag&16) && (n_seqs&1) == 0) continue;
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