added -B/-E to trimfq for keeping first/last INT bp and also -s for shortest read

LICENSE

@@ -0,0 +1,19 @@
+The MIT License
+Copyright (c) 20082-2012 by Heng Li <lh3@me.com>
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Makefile

@@ -1,13 +1,10 @@
 CC=gcc
 CFLAGS=-g -Wall -O2 -Wno-unused-function
 
-all:seqtk trimadap
+all:seqtk
 
 seqtk:seqtk.c khash.h kseq.h
 		$(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm
 
-trimadap:trimadap.c kseq.h ksw.h
-		$(CC) $(CFLAGS) ksw.c trimadap.c -o $@ -lz -lm
-
 clean:
 		rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*

README.md

@@ -3,7 +3,12 @@ Introduction
 
 Seqtk is a fast and lightweight tool for processing sequences in the FASTA or
 FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be
-optionally compressed by gzip.
+optionally compressed by gzip. To install `seqtk`,
+```sh
+git clone https://github.com/lh3/seqtk.git;
+cd seqtk; make
+```
+The only library dependency is zlib.
 
 Seqtk Examples
 --------------
@@ -54,3 +59,6 @@ Seqtk Examples
 
         seqtk trimfq -b 5 -e 10 in.fa > out.fa
 
+* Keep the 50bp from right end of each read by trimming the rest and if the trimmed read length ends up having less the 20bp then the first 20 bp should be kept only:
+
+          seqtk trimfq -E 50 -s 20 in.fq > out.fq

kseq.h

@@ -23,7 +23,7 @@
    SOFTWARE.
 */
 
-/* Last Modified: 05MAR2012 */
+/* Last Modified: 2017-02-11 */
 
 #ifndef AC_KSEQ_H
 #define AC_KSEQ_H
@@ -39,44 +39,44 @@
 
 #define __KS_TYPE(type_t) \
 	typedef struct __kstream_t { \
-		int begin, end; \
-		int is_eof:2, bufsize:30; \
-		type_t f; \
 		unsigned char *buf; \
+		int begin, end, is_eof; \
+		type_t f; \
 	} kstream_t;
 
+#define ks_err(ks) ((ks)->end < 0)
 #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
 #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
 
-#define __KS_BASIC(SCOPE, type_t, __bufsize) \
-	SCOPE kstream_t *ks_init(type_t f) \
+#define __KS_BASIC(type_t, __bufsize) \
+	static inline kstream_t *ks_init(type_t f) \
 	{ \
 		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
-		ks->f = f; ks->bufsize = __bufsize; \
+		ks->f = f; \
 		ks->buf = (unsigned char*)malloc(__bufsize); \
 		return ks; \
 	} \
-	SCOPE void ks_destroy(kstream_t *ks) \
+	static inline void ks_destroy(kstream_t *ks) \
 	{ \
-		if (!ks) return; \
-		free(ks->buf); \
-		free(ks); \
+		if (ks) { \
+			free(ks->buf); \
+			free(ks); \
+		} \
 	}
 
-#define __KS_INLINED(__read) \
+#define __KS_GETC(__read, __bufsize) \
 	static inline int ks_getc(kstream_t *ks) \
 	{ \
-		if (ks->is_eof && ks->begin >= ks->end) return -1; \
+		if (ks_err(ks)) return -3; \
+		if (ks_eof(ks)) return -1; \
 		if (ks->begin >= ks->end) { \
 			ks->begin = 0; \
-			ks->end = __read(ks->f, ks->buf, ks->bufsize); \
-			if (ks->end < ks->bufsize) ks->is_eof = 1; \
-			if (ks->end == 0) return -1; \
+			ks->end = __read(ks->f, ks->buf, __bufsize); \
+			if (ks->end == 0) { ks->is_eof = 1; return -1; } \
+			else if (ks->end < 0) { ks->is_eof = 1; return -3; } \
 		} \
 		return (int)ks->buf[ks->begin++]; \
-	} \
-	static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
-	{ return ks_getuntil2(ks, delimiter, str, dret, 0); }
+	}
 
 #ifndef KSTRING_T
 #define KSTRING_T kstring_t
@@ -90,24 +90,25 @@ typedef struct __kstring_t {
 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
 #endif
 
-#define __KS_GETUNTIL(SCOPE, __read) \
-	SCOPE int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append)  \
+#define __KS_GETUNTIL(__read, __bufsize) \
+	static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
 	{ \
+		int gotany = 0; \
 		if (dret) *dret = 0; \
 		str->l = append? str->l : 0; \
-		if (ks->begin >= ks->end && ks->is_eof) return -1; \
 		for (;;) { \
 			int i; \
+			if (ks_err(ks)) return -3; \
 			if (ks->begin >= ks->end) { \
 				if (!ks->is_eof) { \
 					ks->begin = 0; \
-					ks->end = __read(ks->f, ks->buf, ks->bufsize); \
-					if (ks->end < ks->bufsize) ks->is_eof = 1; \
-					if (ks->end == 0) break; \
+					ks->end = __read(ks->f, ks->buf, __bufsize); \
+					if (ks->end == 0) { ks->is_eof = 1; break; } \
+					if (ks->end == -1) { ks->is_eof = 1; return -3; } \
 				} else break; \
 			} \
-			if (delimiter == KS_SEP_LINE) {  \
-				for (i = ks->begin; i < ks->end; ++i)  \
+			if (delimiter == KS_SEP_LINE) { \
+				for (i = ks->begin; i < ks->end; ++i) \
 					if (ks->buf[i] == '\n') break; \
 			} else if (delimiter > KS_SEP_MAX) { \
 				for (i = ks->begin; i < ks->end; ++i) \
@@ -117,123 +118,117 @@ typedef struct __kstring_t {
 					if (isspace(ks->buf[i])) break; \
 			} else if (delimiter == KS_SEP_TAB) { \
 				for (i = ks->begin; i < ks->end; ++i) \
-					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break;  \
+					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
 			} else i = 0; /* never come to here! */ \
 			if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \
 				str->m = str->l + (i - ks->begin) + 1; \
 				kroundup32(str->m); \
 				str->s = (char*)realloc(str->s, str->m); \
 			} \
-			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin);  \
+			gotany = 1; \
+			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
 			str->l = str->l + (i - ks->begin); \
 			ks->begin = i + 1; \
 			if (i < ks->end) { \
 				if (dret) *dret = ks->buf[i]; \
 				break; \
 			} \
 		} \
+		if (!gotany && ks_eof(ks)) return -1; \
 		if (str->s == 0) { \
 			str->m = 1; \
 			str->s = (char*)calloc(1, 1); \
 		} else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \
-		str->s[str->l] = '\0';											\
+		str->s[str->l] = '\0'; \
 		return str->l; \
-	}
-
-#define KSTREAM_INIT2(SCOPE, type_t, __read, __bufsize) \
-	__KS_TYPE(type_t) \
-	__KS_BASIC(SCOPE, type_t, __bufsize) \
-	__KS_GETUNTIL(SCOPE, __read) \
-	__KS_INLINED(__read)
-
-#define KSTREAM_INIT(type_t, __read, __bufsize) KSTREAM_INIT2(static, type_t, __read, __bufsize)
+	} \
+	static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+	{ return ks_getuntil2(ks, delimiter, str, dret, 0); }
 
-#define KSTREAM_DECLARE(type_t, __read) \
+#define KSTREAM_INIT(type_t, __read, __bufsize) \
 	__KS_TYPE(type_t) \
-	extern int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append); \
-	extern kstream_t *ks_init(type_t f); \
-	extern void ks_destroy(kstream_t *ks); \
-	__KS_INLINED(__read)
-
-/******************
- * FASTA/Q parser *
- ******************/
+	__KS_BASIC(type_t, __bufsize) \
+	__KS_GETC(__read, __bufsize) \
+	__KS_GETUNTIL(__read, __bufsize)
 
 #define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
 
-#define __KSEQ_BASIC(SCOPE, type_t)										\
-	SCOPE kseq_t *kseq_init(type_t fd)									\
-	{																	\
-		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));					\
-		s->f = ks_init(fd);												\
-		return s;														\
-	}																	\
-	SCOPE void kseq_destroy(kseq_t *ks)									\
-	{																	\
-		if (!ks) return;												\
+#define __KSEQ_BASIC(SCOPE, type_t) \
+	SCOPE kseq_t *kseq_init(type_t fd) \
+	{ \
+		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
+		s->f = ks_init(fd); \
+		return s; \
+	} \
+	SCOPE void kseq_destroy(kseq_t *ks) \
+	{ \
+		if (!ks) return; \
 		free(ks->name.s); free(ks->comment.s); free(ks->seq.s);	free(ks->qual.s); \
-		ks_destroy(ks->f);												\
-		free(ks);														\
+		ks_destroy(ks->f); \
+		free(ks); \
 	}
 
 /* Return value:
    >=0  length of the sequence (normal)
    -1   end-of-file
    -2   truncated quality string
+   -3   error reading stream
  */
 #define __KSEQ_READ(SCOPE) \
 	SCOPE int kseq_read(kseq_t *seq) \
 	{ \
-		int c; \
+		int c,r; \
 		kstream_t *ks = seq->f; \
 		if (seq->last_char == 0) { /* then jump to the next header line */ \
-			while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
-			if (c == -1) return -1; /* end of file */ \
+			while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '@'); \
+			if (c < 0) return c; /* end of file or error*/ \
 			seq->last_char = c; \
 		} /* else: the first header char has been read in the previous call */ \
 		seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
-		if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
+		if ((r=ks_getuntil(ks, 0, &seq->name, &c)) < 0) return r;  /* normal exit: EOF or error */ \
 		if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
 		if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
 			seq->seq.m = 256; \
 			seq->seq.s = (char*)malloc(seq->seq.m); \
 		} \
-		while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
+		while ((c = ks_getc(ks)) >= 0 && c != '>' && c != '+' && c != '@') { \
 			if (c == '\n') continue; /* skip empty lines */ \
 			seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
 			ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
 		} \
-		if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */	\
+		if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
 		if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
 			seq->seq.m = seq->seq.l + 2; \
 			kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
 			seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
 		} \
 		seq->seq.s[seq->seq.l] = 0;	/* null terminated string */ \
-		if (c != '+') return seq->seq.l; /* FASTA */ \
+		seq->is_fastq = (c == '+'); \
+		if (!seq->is_fastq) return seq->seq.l; /* FASTA */ \
 		if (seq->qual.m < seq->seq.m) {	/* allocate memory for qual in case insufficient */ \
 			seq->qual.m = seq->seq.m; \
 			seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
 		} \
-		while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
+		while ((c = ks_getc(ks)) >= 0 && c != '\n'); /* skip the rest of '+' line */ \
 		if (c == -1) return -2; /* error: no quality string */ \
-		while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
+		while ((c = ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l)); \
+		if (c == -3) return -3; /* stream error */ \
 		seq->last_char = 0;	/* we have not come to the next header line */ \
 		if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
 		return seq->seq.l; \
 	}
 
-#define __KSEQ_TYPE(type_t)						\
-	typedef struct {							\
-		kstring_t name, comment, seq, qual;		\
-		int last_char;							\
-		kstream_t *f;							\
+#define __KSEQ_TYPE(type_t) \
+	typedef struct { \
+		kstring_t name, comment, seq, qual; \
+		int last_char, is_fastq; \
+		kstream_t *f; \
 	} kseq_t;
 
-#define KSEQ_INIT2(SCOPE, type_t, __read)		\
-	KSTREAM_INIT2(SCOPE, type_t, __read, 16384)	\
-	__KSEQ_TYPE(type_t)							\
-	__KSEQ_BASIC(SCOPE, type_t)					\
+#define KSEQ_INIT2(SCOPE, type_t, __read) \
+	KSTREAM_INIT(type_t, __read, 16384) \
+	__KSEQ_TYPE(type_t) \
+	__KSEQ_BASIC(SCOPE, type_t) \
 	__KSEQ_READ(SCOPE)
 
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)