v0.2 - options and bug fixes

.gitignore

@@ -50,3 +50,6 @@ modules.order
 Module.symvers
 Mkfile.old
 dkms.conf
+
+# backups
+*~

Makefile

@@ -0,0 +1,31 @@
+
+CC = gcc
+CFLAGS = -Wall -Wextra -O3 -std=c99 
+LIBS = -lz -lm
+
+EXE = snp-dists
+PREFIX = /usr/local
+TESTDIR = test
+
+.PHONY: check clean
+.DEFAULT: all
+
+all: $(EXE) check
+
+$(EXE): main.c 
+	$(CC) $(CFLAGS) -o $(EXE) $^ $(LIBS)
+
+main.c: kseq.h
+
+install: $(EXE)
+	install -v -t $(PREFIX)/bin $(EXE)
+
+clean:
+	$(RM) *~ *.o $(EXE)
+
+check:
+	./$(EXE) $(TESTDIR)/singleton.aln
+	./$(EXE) $(TESTDIR)/good.aln
+	./$(EXE) $(TESTDIR)/gzip.aln.gz
+	./$(EXE) -b -c -q $(TESTDIR)/good.aln
+	./$(EXE) -v

README.md

@@ -5,7 +5,7 @@ Convert a FASTA alignment to SNP distance matrix
 # Quick Start
 
 ```
-% cat test.aln
+% cat test/good.aln
 
 >seq1
 AGTCAGTC
@@ -16,13 +16,13 @@ AGTGAGTA
 >seq4
 TGTTAGAC
 
-% snp-dists test.aln > distances.tab
+% snp-dists test/good.aln > distances.tab
 
 Read 4 sequences of length 8
 
 % cat distances.tab
 
-SNP-DIST 0.1    seq1    seq2    seq3    seq4
+snp-dists 0.2   seq1    seq2    seq3    seq4
 seq1            0       1       2       3
 seq2            1       0       3       4
 seq3            2       3       0       4
@@ -31,13 +31,65 @@ seq4            3       4       4       0
 
 # Installation
 
-`snp-dists` is written in ANSI C and only depends on `libz`.
+`snp-dists` is written in C to the C99 standard and only depends on `libz`.
 
-```
+```bash
 git clone https://github.com/tseemann/snp-dists.git
 cd snp-dists/src
 make
-cp snp-dists /usr/local/bin
+# optionally install to /usr/local/bin 
+make PREFIX=/usr/local install  
+```
+
+# Options
+
+## snp-dists -h (help)
+
+```
+SYNOPSIS
+  Pairwise SNP distance matrix from a FASTA alignment
+USAGE
+  snp-dists [options] alignment.fasta > matrix.tsv
+OPTIONS
+  -h    Show this help
+  -v    Print version and exit
+  -q    Quiet mode; do not print progress information
+  -c    Output CSV instead of TSV
+  -b    Blank top left corner cell instead of 'snp-dists 0.2'
+URL
+  https://github.com/tseemann/snp-dists (Torsten Seemann)
+```
+
+## snp-dists -v (version)
+
+Prints the name and version separated by a space in standard Unix fashion.
+
+```
+snp-dists 0.2
+```
+
+## snp-dists -q (quiet mode)
+
+Don't print informational messages, only errors.
+
+## snp-dists -c good.aln (CSV instead of TSV)
+
+```
+snp-dists 0.2,seq1,seq2,seq3,seq4
+seq1,0,1,2,3
+seq2,1,0,3,4
+seq3,2,3,0,4
+seq4,3,4,4,0
+```
+
+## snp-dists -b good.aln (Omit the toolname/version)
+
+```
+        seq1    seq2    seq3    seq4
+seq1    0       1       2       3
+seq2    1       0       3       4
+seq3    2       3       0       4
+seq4    3       4       4       0
 ```
 
 # Issues

kseq.h

@@ -0,0 +1,242 @@
+/* The MIT License
+
+   Copyright (c) 2008, 2009, 2011 Attractive Chaos <[email protected]>
+
+   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.
+*/
+
+/* Last Modified: 05MAR2012 */
+
+#ifndef AC_KSEQ_H
+#define AC_KSEQ_H
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB   1 // isspace() && !' '
+#define KS_SEP_LINE  2 // line separator: "\n" (Unix) or "\r\n" (Windows)
+#define KS_SEP_MAX   2
+
+#define __KS_TYPE(type_t)						\
+	typedef struct __kstream_t {				\
+		unsigned char *buf;						\
+		int begin, end, is_eof;					\
+		type_t f;								\
+	} kstream_t;
+
+#define ks_err(ks) ((ks)->end == -1)
+#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(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->buf = (unsigned char*)malloc(__bufsize);				\
+		return ks;													\
+	}																\
+	static inline void ks_destroy(kstream_t *ks)					\
+	{																\
+		if (ks) {													\
+			free(ks->buf);											\
+			free(ks);												\
+		}															\
+	}
+
+#define __KS_GETC(__read, __bufsize)						\
+	static inline int ks_getc(kstream_t *ks)				\
+	{														\
+		if (ks_err(ks)) return -3;							\
+		if (ks->is_eof && ks->begin >= ks->end) return -1;	\
+		if (ks->begin >= ks->end) {							\
+			ks->begin = 0;									\
+			ks->end = __read(ks->f, ks->buf, __bufsize);	\
+			if (ks->end == 0) { ks->is_eof = 1; return -1;}	\
+			if (ks->end == -1) { ks->is_eof = 1; return -3;}\
+		}													\
+		return (int)ks->buf[ks->begin++];					\
+	}
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	size_t l, m;
+	char *s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#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;									\
+		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, __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 (ks->buf[i] == '\n') break; \
+			} else if (delimiter > KS_SEP_MAX) {						\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					if (ks->buf[i] == delimiter) break;					\
+			} else if (delimiter == KS_SEP_SPACE) {						\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					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; \
+			} 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);				\
+			}															\
+			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';											\
+		return str->l;													\
+	} \
+	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_INIT(type_t, __read, __bufsize) \
+	__KS_TYPE(type_t)							\
+	__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;												\
+		free(ks->name.s); free(ks->comment.s); free(ks->seq.s);	free(ks->qual.s); \
+		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,r; \
+		kstream_t *ks = seq->f; \
+		if (seq->last_char == 0) { /* then jump to the next header line */ \
+			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 ((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)) >= 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 (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 */ \
+		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)) >= 0 && c != '\n'); /* skip the rest of '+' line */ \
+		if (c == -1) return -2; /* error: no quality string */ \
+		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;							\
+	} kseq_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)
+
+#define KSEQ_DECLARE(type_t) \
+	__KS_TYPE(type_t) \
+	__KSEQ_TYPE(type_t) \
+	extern kseq_t *kseq_init(type_t fd); \
+	void kseq_destroy(kseq_t *ks); \
+	int kseq_read(kseq_t *seq);
+
+#endif