Commit 4a49cae3 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 0.1.6+git20171023

parent 974be90f

LICENSE

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+21 −0
Original line number Diff line number Diff line 
The MIT License (MIT)



Copyright (c) 2015 Brent Pedersen and Aaron Quinlan



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.

grabix.cpp

+19 −11
Original line number Diff line number Diff line 
#include <cstdlib>

#include <iostream>

#include <stdio.h>

#include <fstream>

#include <vector>

#include <unistd.h>
@@ -56,6 +57,12 @@ random access via the BGZF seek utility 
*/

int create_grabix_index(string bgzf_file)

{

    if (!bgzf_is_bgzf(bgzf_file.c_str()))

    {

        cerr << "[grabix] " << bgzf_file << " doesn't exist or wasn't compressed with bgzip" << endl;

        exit (1);

    }



    BGZF *bgzf_fp = bgzf_open(bgzf_file.c_str(), "r");

    if (bgzf_fp == NULL)

    {
@@ -64,7 +71,7 @@ int create_grabix_index(string bgzf_file) 
    }



    // create an index for writing

    string index_file_name = bgzf_file + ".gbi";

    string index_file_name = bgzf_file + ".gbi.tmp";

    ofstream index_file(index_file_name.c_str(), ios::out);



    // add the offset for the end of the header to the index
@@ -92,15 +99,15 @@ int create_grabix_index(string bgzf_file) 
    int64_t total_lines = 1;

    vector<int64_t> chunk_positions;

    chunk_positions.push_back (prev_offset);

    bool eof = false;

    int eof = 1;

    while (true)

    {

        // grab the next line and store the offset

        eof = bgzf_getline_counting(bgzf_fp);

        eof = bgzf_getline(bgzf_fp, '\n', line);

        offset = bgzf_tell(bgzf_fp);

        chunk_count++;

        // stop if we have encountered an empty line

        if (eof)

        if (eof < 0 || offset == prev_offset)

        {

            if (bgzf_check_EOF(bgzf_fp) == 1) {

                if (offset > prev_offset) {
@@ -109,6 +116,7 @@ int create_grabix_index(string bgzf_file) 
                }

                break;

            }

            break;

        }

        // store the offset of this chunk start

        else if (chunk_count == CHUNK_SIZE)
@@ -129,7 +137,7 @@ int create_grabix_index(string bgzf_file) 
    }

    index_file.close();



    return EXIT_SUCCESS;

    return std::rename((bgzf_file + ".gbi.tmp").c_str(), (bgzf_file + ".gbi").c_str());

}



/*
@@ -206,7 +214,7 @@ int grab(string bgzf_file, int64_t from_line, int64_t to_line) 
        line->l = 0;

        line->m = 0;



        while ((status = bgzf_getline(bgzf_fp, '\n', line)) != 0)

        while ((status = bgzf_getline(bgzf_fp, '\n', line)) > 0)

        {

            if (line->s[0] == '#')

                printf("%s\n", line->s);

grabix.h

+1 −1
Original line number Diff line number Diff line
@@ -7,7 +7,7 @@ using namespace std; 
#include "bgzf.h"





#define VERSION "0.1.6"

#define VERSION "0.1.8"

// we only want to store the offset for every 10000th

// line. otherwise, were we to store the position of every

// line in the file, the index could become very large for

test.sh

+21 −3
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@@ -3,17 +3,35 @@ make 
FQ=test.cnt.gz

rm -f ${FQ}{,.gbi}



lines=50000

lines=500000

python tests/make-test-fastq.py $lines | bgzip -c > $FQ

./grabix index $FQ

echo "indexing"

time ./grabix index $FQ

echo "indexed"

python tests/test-fastq.py $FQ

a=$(grabix grab test.cnt.gz $(($lines * 4)))

a=$(./grabix grab test.cnt.gz $(($lines * 4)))

b=$(zless $FQ | tail -1)

if [[ "$a" != "$b" ]]; then

	echo FAIL last record

    exit 1

else

	echo OK last record

fi

rm -f ${FQ}{,.gbi}



rm -f tests/empty.fastq.gz.gbi

./grabix index tests/empty.fastq.gz



a=$(cat tests/empty.fastq.gz.gbi | awk 'NR == 2')

if [[ "$a" != "16" ]]; then

    echo FAIL index wrong size

    exit 1

else

    echo "OK index size"

fi







for V in  \

	test.PLs.vcf \

	test.auto_dom.no_parents.2.vcf \

tests/empty.fastq.gz

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