Commit 70b5efe2 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.33+git20150314.f3d6ae3

parent ef4cf6ee

Makefile

+1 −1
Original line number Diff line number Diff line
@@ -35,7 +35,7 @@ distclean: clean 
	rm -rf *.tar.gz



dist:

	tar -zcf $(ARCHIVE).tar.gz src Makefile

	tar -zcf $(ARCHIVE).tar.gz src Makefile README.md sickle.xml LICENSE



build: sliding.o trim_single.o trim_paired.o sickle.o print_record.o

	$(CC) $(CFLAGS) $(LDFLAGS) $(OPT) $? -o sickle $(LIBS)

README.md

+5 −0
Original line number Diff line number Diff line
@@ -94,6 +94,7 @@ truncation of sequences with Ns. 
    sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -q 33 -l 40

    sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -x -n

    sickle se -t sanger -g -f input_file.fastq -o trimmed_output_file.fastq.gz

    sickle se --fastq-file input_file.fastq --qual-type sanger --output-file trimmed_output_file.fastq



### Sickle Paired End (`sickle pe`)
@@ -134,3 +135,7 @@ enable truncation of sequences with Ns. 
    -s trimmed_singles_file.fastq.gz



    sickle pe -c combo.fastq -t sanger -M combo_trimmed_all.fastq



    sickle pe --pe-file1 input_file1.fastq --pe-file2 input_file2.fastq --qual-type sanger \

    --output-pe1 trimmed_output_file1.fastq --output-pe2 trimmed_output_file2.fastq \

    --output-single trimmed_singles_file.fastq

sickle.xml

+0 −1
Original line number Diff line number Diff line
@@ -69,7 +69,6 @@ 
		-n

		#end if



		--quiet

	</command>



	<inputs>

src/kseq.h

+6 −1
Original line number Diff line number Diff line
@@ -191,6 +191,11 @@ typedef struct __kstring_t { 
   }                                                                    \

   }                                                                    \

     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 enough memory */	\

src/trim_paired.c

+19 −14
Original line number Diff line number Diff line
@@ -18,20 +18,20 @@ int paired_length_threshold = 20; 


static struct option paired_long_options[] = {

    {"qual-type", required_argument, 0, 't'},

    {"pe-file1", optional_argument, 0, 'f'},

    {"pe-file2", optional_argument, 0, 'r'},

    {"pe-combo", optional_argument, 0, 'c'},

    {"output-pe1", optional_argument, 0, 'o'},

    {"output-pe2", optional_argument, 0, 'p'},

    {"output-single", optional_argument, 0, 's'},

    {"output-combo", optional_argument, 0, 'm'},

    {"qual-threshold", optional_argument, 0, 'q'},

    {"length-threshold", optional_argument, 0, 'l'},

    {"no-fiveprime", optional_argument, 0, 'x'},

    {"truncate-n", optional_argument, 0, 'n'},

    {"gzip-output", optional_argument, 0, 'g'},

    {"output-combo-all", optional_argument, 0, 'M'},

    {"quiet", optional_argument, 0, 'z'},

    {"pe-file1", required_argument, 0, 'f'},

    {"pe-file2", required_argument, 0, 'r'},

    {"pe-combo", required_argument, 0, 'c'},

    {"output-pe1", required_argument, 0, 'o'},

    {"output-pe2", required_argument, 0, 'p'},

    {"output-single", required_argument, 0, 's'},

    {"output-combo", required_argument, 0, 'm'},

    {"qual-threshold", required_argument, 0, 'q'},

    {"length-threshold", required_argument, 0, 'l'},

    {"no-fiveprime", no_argument, 0, 'x'},

    {"truncate-n", no_argument, 0, 'n'},

    {"gzip-output", no_argument, 0, 'g'},

    {"output-combo-all", required_argument, 0, 'M'},

    {"quiet", no_argument, 0, 'z'},

    {GETOPT_HELP_OPTION_DECL},

    {GETOPT_VERSION_OPTION_DECL},

    {NULL, 0, NULL, 0}
@@ -117,6 +117,7 @@ int paired_main(int argc, char *argv[]) { 
    int gzip_output = 0;

    int combo_all=0;

    int combo_s=0;

    int total=0;



    while (1) {

        int option_index = 0;
@@ -375,6 +376,7 @@ int paired_main(int argc, char *argv[]) { 


        p1cut = sliding_window(fqrec1, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, debug);

        p2cut = sliding_window(fqrec2, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, debug);

        total += 2;



        if (debug) printf("p1cut: %d,%d\n", p1cut->five_prime_cut, p1cut->three_prime_cut);

        if (debug) printf("p2cut: %d,%d\n", p2cut->five_prime_cut, p2cut->three_prime_cut);
@@ -478,6 +480,9 @@ int paired_main(int argc, char *argv[]) { 
    }



    if (!quiet) {

        if (infn1 && infn2) fprintf(stdout, "\nPE forward file: %s\nPE reverse file: %s\n", infn1, infn2);

        if (infnc) fprintf(stdout, "\nPE interleaved file: %s\n", infnc);

        fprintf(stdout, "\nTotal input FastQ records: %d (%d pairs)\n", total, (total / 2));

        fprintf(stdout, "\nFastQ paired records kept: %d (%d pairs)\n", kept_p, (kept_p / 2));

        if (pec) fprintf(stdout, "FastQ single records kept: %d\n", (kept_s1 + kept_s2));

        else fprintf(stdout, "FastQ single records kept: %d (from PE1: %d, from PE2: %d)\n", (kept_s1 + kept_s2), kept_s1, kept_s2);