New upstream version 0.1.7 (bb2e5a92) · Commits · Debian Med / grabix

grabix.cpp

+5 −5

Original line number	Diff line number	Diff line
		@@ -107,7 +107,7 @@ int create_grabix_index(string bgzf_file)
		offset = bgzf_tell (bgzf_fp);
		chunk_count++;
		// stop if we have encountered an empty line
		if (eof < 0 \|\| offset == prev_offset)
		if (eof <= 0)
		{
		if (bgzf_check_EOF(bgzf_fp) == 1) {
		if (offset > prev_offset) {
		@@ -116,7 +116,7 @@ int create_grabix_index(string bgzf_file)
		}
		break;
		}
		break;
		//break;
		}
		// store the offset of this chunk start
		else if (chunk_count == CHUNK_SIZE)
		@@ -214,7 +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);

+1 −1

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


		#define VERSION "0.1.8"
		#define VERSION "0.1.7"
		// 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

+1 −17

Original line number	Diff line number	Diff line
		@@ -9,29 +9,13 @@ 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 \

deleted100644 → 0

−79 B

File deleted.