[med-svn] [fastaq] branch master updated (ebff001 -> 7b74436)
Jorge Soares
jssoares-guest at moszumanska.debian.org
Wed Oct 8 10:54:01 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a change to branch master
in repository fastaq.
from ebff001 Move debian/upstream to debian/upstream/metadata
new 7b74436 Removed all the source code
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
debian/changelog | 4 +-
debian/watch | 4 +-
fastaq/__init__.py | 2 -
fastaq/intervals.py | 117 -----
fastaq/sequences.py | 549 --------------------
fastaq/tasks.py | 556 ---------------------
fastaq/tests/data/sequences_test.embl | 203 --------
fastaq/tests/data/sequences_test.embl.bad | 202 --------
fastaq/tests/data/sequences_test.embl.bad2 | 202 --------
fastaq/tests/data/sequences_test.embl.to_fasta | 64 ---
fastaq/tests/data/sequences_test.fa | 19 -
fastaq/tests/data/sequences_test.fa.ids | 4 -
fastaq/tests/data/sequences_test.fa.qual | 17 -
fastaq/tests/data/sequences_test.fa.qual.bad | 17 -
fastaq/tests/data/sequences_test.fasta_to_fastq.fq | 16 -
fastaq/tests/data/sequences_test.gbk | 170 -------
fastaq/tests/data/sequences_test.gbk.to_fasta | 10 -
fastaq/tests/data/sequences_test.line_length3.fa | 12 -
fastaq/tests/data/sequences_test_3-per-line.fa | 19 -
.../tests/data/sequences_test_cap_to_read_pairs.fa | 16 -
.../sequences_test_cap_to_read_pairs.fa.paired.gz | Bin 92 -> 0 bytes
...sequences_test_cap_to_read_pairs.fa.unpaired.gz | Bin 92 -> 0 bytes
.../tests/data/sequences_test_deinterleaved_1.fa | 4 -
.../tests/data/sequences_test_deinterleaved_2.fa | 4 -
.../data/sequences_test_deinterleaved_bad2_1.fa | 2 -
.../data/sequences_test_deinterleaved_bad2_2.fa | 4 -
.../data/sequences_test_deinterleaved_bad_1.fa | 4 -
.../data/sequences_test_deinterleaved_bad_2.fa | 2 -
fastaq/tests/data/sequences_test_empty_file | 0
.../tests/data/sequences_test_enumerate_names.fa | 8 -
...quences_test_enumerate_names.fa.out.keep_suffix | 8 -
.../sequences_test_enumerate_names.fa.out.start.1 | 8 -
...test_enumerate_names.fa.out.start.1.rename_file | 5 -
.../sequences_test_enumerate_names.fa.out.start.2 | 8 -
fastaq/tests/data/sequences_test_extend_gaps.fa | 8 -
.../tests/data/sequences_test_extend_gaps.fa.out | 4 -
fastaq/tests/data/sequences_test_fai_test.fa | 8 -
fastaq/tests/data/sequences_test_fai_test.fa.fai | 4 -
fastaq/tests/data/sequences_test_fail_no_AT.fq | 5 -
fastaq/tests/data/sequences_test_fail_no_plus.fq | 4 -
fastaq/tests/data/sequences_test_fail_no_qual.fq | 3 -
fastaq/tests/data/sequences_test_fail_no_seq.fq | 5 -
...sequences_test_fastaq_replace_bases.expected.fa | 2 -
.../data/sequences_test_fastaq_replace_bases.fa | 2 -
...sequences_test_fastaq_to_quasr_primers.expected | 2 -
.../data/sequences_test_fastaq_to_quasr_primers.fa | 4 -
.../data/sequences_test_filter_by_ids_file.fa | 8 -
.../sequences_test_filter_by_ids_file.fa.filtered | 4 -
...nces_test_filter_by_ids_file.fa.filtered.invert | 4 -
.../data/sequences_test_filter_by_ids_file.fa.ids | 2 -
.../tests/data/sequences_test_filter_by_regex.fa | 10 -
.../sequences_test_filter_by_regex.first-char-a.fa | 6 -
...sequences_test_filter_by_regex.first-of-pair.fa | 4 -
.../data/sequences_test_filter_by_regex.numeric.fa | 2 -
.../data/sequences_test_get_seqs_flanking_gaps.fa | 4 -
.../sequences_test_get_seqs_flanking_gaps.fa.out | 3 -
fastaq/tests/data/sequences_test_gffv3.gff | 9 -
fastaq/tests/data/sequences_test_gffv3.gff.fasta | 4 -
.../tests/data/sequences_test_gffv3.gff.to_fasta | 4 -
.../data/sequences_test_gffv3.no_FASTA_line.gff | 8 -
...sequences_test_gffv3.no_FASTA_line.gff.to_fasta | 4 -
.../tests/data/sequences_test_gffv3.no_seq.2.gff | 6 -
fastaq/tests/data/sequences_test_gffv3.no_seq.gff | 4 -
fastaq/tests/data/sequences_test_good_file.fq | 11 -
.../data/sequences_test_good_file.fq.to_fasta | 4 -
.../tests/data/sequences_test_good_file_mira.xml | 13 -
fastaq/tests/data/sequences_test_interleaved.fa | 8 -
fastaq/tests/data/sequences_test_interleaved.fq | 16 -
.../tests/data/sequences_test_interleaved_bad.fa | 6 -
fastaq/tests/data/sequences_test_length_filter.fa | 6 -
.../sequences_test_length_filter.min-0.max-1.fa | 0
.../sequences_test_length_filter.min-0.max-inf.fa | 6 -
.../sequences_test_length_filter.min-4.max-4.fa | 2 -
.../sequences_test_make_random_contigs.default.fa | 4 -
.../sequences_test_make_random_contigs.first-42.fa | 4 -
...ces_test_make_random_contigs.name-by-letters.fa | 56 ---
.../sequences_test_make_random_contigs.prefix-p.fa | 4 -
fastaq/tests/data/sequences_test_not_a_fastaq_file | 1 -
fastaq/tests/data/sequences_test_one-per-line.fa | 14 -
.../tests/data/sequences_test_phylip.interleaved | 8 -
.../sequences_test_phylip.interleaved.to_fasta | 6 -
.../tests/data/sequences_test_phylip.interleaved2 | 7 -
.../sequences_test_phylip.interleaved2.to_fasta | 6 -
.../data/sequences_test_phylip.made_by_seaview | 6 -
.../sequences_test_phylip.made_by_seaview.to_fasta | 6 -
fastaq/tests/data/sequences_test_phylip.sequential | 7 -
.../data/sequences_test_phylip.sequential.to_fasta | 6 -
fastaq/tests/data/sequences_test_revcomp.fa | 8 -
fastaq/tests/data/sequences_test_search_string.fa | 2 -
.../data/sequences_test_search_string.fa.hits | 4 -
.../tests/data/sequences_test_split_fixed_size.fa | 12 -
.../sequences_test_split_fixed_size.fa.split.1 | 2 -
.../sequences_test_split_fixed_size.fa.split.2 | 2 -
.../sequences_test_split_fixed_size.fa.split.3 | 2 -
.../sequences_test_split_fixed_size.fa.split.4 | 2 -
.../sequences_test_split_fixed_size.fa.split.5 | 4 -
.../sequences_test_split_fixed_size.fa.split.6 | 2 -
...sequences_test_split_fixed_size.fa.split.coords | 2 -
...test_split_fixed_size.fa.split.skip_if_all_Ns.1 | 2 -
...test_split_fixed_size.fa.split.skip_if_all_Ns.2 | 2 -
...test_split_fixed_size.fa.split.skip_if_all_Ns.3 | 4 -
...test_split_fixed_size.fa.split.skip_if_all_Ns.4 | 2 -
...split_fixed_size.fa.split.skip_if_all_Ns.coords | 1 -
fastaq/tests/data/sequences_test_split_test.fa | 8 -
fastaq/tests/data/sequences_test_split_test.fa.2.1 | 2 -
fastaq/tests/data/sequences_test_split_test.fa.2.2 | 2 -
fastaq/tests/data/sequences_test_split_test.fa.2.3 | 2 -
fastaq/tests/data/sequences_test_split_test.fa.2.4 | 2 -
fastaq/tests/data/sequences_test_split_test.fa.3.1 | 4 -
fastaq/tests/data/sequences_test_split_test.fa.3.2 | 2 -
fastaq/tests/data/sequences_test_split_test.fa.3.3 | 2 -
fastaq/tests/data/sequences_test_split_test.fa.4.1 | 4 -
fastaq/tests/data/sequences_test_split_test.fa.4.2 | 2 -
fastaq/tests/data/sequences_test_split_test.fa.4.3 | 2 -
fastaq/tests/data/sequences_test_split_test.fa.6.1 | 6 -
fastaq/tests/data/sequences_test_split_test.fa.6.2 | 2 -
.../data/sequences_test_split_test.fa.6.limit2.1 | 4 -
.../data/sequences_test_split_test.fa.6.limit2.2 | 2 -
.../data/sequences_test_split_test.fa.6.limit2.3 | 2 -
.../tests/data/sequences_test_split_test.long.fa | 4 -
.../data/sequences_test_split_test.long.fa.2.1 | 2 -
.../data/sequences_test_split_test.long.fa.2.2 | 2 -
.../data/sequences_test_strip_after_whitespace.fa | 6 -
...quences_test_strip_after_whitespace.fa.to_fasta | 6 -
.../data/sequences_test_strip_illumina_suffix.fq | 12 -
...equences_test_strip_illumina_suffix.fq.stripped | 12 -
.../tests/data/sequences_test_to_unique_by_id.fa | 11 -
.../data/sequences_test_to_unique_by_id.fa.out | 6 -
fastaq/tests/data/sequences_test_translate.fa | 2 -
.../tests/data/sequences_test_translate.fa.frame0 | 3 -
.../tests/data/sequences_test_translate.fa.frame1 | 3 -
.../tests/data/sequences_test_translate.fa.frame2 | 3 -
fastaq/tests/data/sequences_test_trim_Ns_at_end.fa | 10 -
.../data/sequences_test_trim_Ns_at_end.fa.trimmed | 8 -
fastaq/tests/data/sequences_test_trimmed.fq | 8 -
fastaq/tests/data/sequences_test_untrimmed.fq | 16 -
fastaq/tests/data/utils_test_file_transpose.txt | 5 -
fastaq/tests/data/utils_test_file_transposed.txt | 3 -
fastaq/tests/data/utils_test_not_really_zipped.gz | 1 -
fastaq/tests/data/utils_test_scaffolds.fa | 8 -
.../data/utils_test_scaffolds.fa.to_contigs.fa | 10 -
..._test_scaffolds.fa.to_contigs.number_contigs.fa | 10 -
fastaq/tests/data/utils_test_system_call.txt | 1 -
fastaq/tests/intervals_test.py | 212 --------
fastaq/tests/sequences_test.py | 535 --------------------
fastaq/tests/tasks_test.py | 449 -----------------
fastaq/tests/utils_test.py | 80 ---
fastaq/utils.py | 86 ----
{scripts => src}/fastaq_capillary_to_pairs | 0
{scripts => src}/fastaq_chunker | 0
{scripts => src}/fastaq_count_sequences | 0
{scripts => src}/fastaq_deinterleave | 0
{scripts => src}/fastaq_enumerate_names | 0
{scripts => src}/fastaq_extend_gaps | 0
{scripts => src}/fastaq_fasta_to_fastq | 0
{scripts => src}/fastaq_filter | 0
{scripts => src}/fastaq_get_ids | 0
{scripts => src}/fastaq_get_seq_flanking_gaps | 0
{scripts => src}/fastaq_insert_or_delete_bases | 0
{scripts => src}/fastaq_interleave | 0
{scripts => src}/fastaq_make_random_contigs | 0
{scripts => src}/fastaq_replace_bases | 0
{scripts => src}/fastaq_reverse_complement | 0
{scripts => src}/fastaq_scaffolds_to_contigs | 0
{scripts => src}/fastaq_search_for_seq | 0
{scripts => src}/fastaq_split_by_base_count | 0
{scripts => src}/fastaq_strip_illumina_suffix | 0
{scripts => src}/fastaq_to_fasta | 0
{scripts => src}/fastaq_to_mira_xml | 0
{scripts => src}/fastaq_to_perfect_reads | 0
{scripts => src}/fastaq_to_quasr_primers_file | 0
{scripts => src}/fastaq_to_random_subset | 0
{scripts => src}/fastaq_to_tiling_bam | 0
{scripts => src}/fastaq_to_unique_by_id | 0
{scripts => src}/fastaq_translate | 0
{scripts => src}/fastaq_trim_Ns_at_end | 0
{scripts => src}/fastaq_trim_ends | 0
177 files changed, 4 insertions(+), 4215 deletions(-)
delete mode 100644 fastaq/__init__.py
delete mode 100644 fastaq/intervals.py
delete mode 100644 fastaq/sequences.py
delete mode 100644 fastaq/tasks.py
delete mode 100644 fastaq/tests/data/sequences_test.embl
delete mode 100644 fastaq/tests/data/sequences_test.embl.bad
delete mode 100644 fastaq/tests/data/sequences_test.embl.bad2
delete mode 100644 fastaq/tests/data/sequences_test.embl.to_fasta
delete mode 100644 fastaq/tests/data/sequences_test.fa
delete mode 100644 fastaq/tests/data/sequences_test.fa.ids
delete mode 100644 fastaq/tests/data/sequences_test.fa.qual
delete mode 100644 fastaq/tests/data/sequences_test.fa.qual.bad
delete mode 100644 fastaq/tests/data/sequences_test.fasta_to_fastq.fq
delete mode 100644 fastaq/tests/data/sequences_test.gbk
delete mode 100644 fastaq/tests/data/sequences_test.gbk.to_fasta
delete mode 100644 fastaq/tests/data/sequences_test.line_length3.fa
delete mode 100644 fastaq/tests/data/sequences_test_3-per-line.fa
delete mode 100644 fastaq/tests/data/sequences_test_cap_to_read_pairs.fa
delete mode 100644 fastaq/tests/data/sequences_test_cap_to_read_pairs.fa.paired.gz
delete mode 100644 fastaq/tests/data/sequences_test_cap_to_read_pairs.fa.unpaired.gz
delete mode 100644 fastaq/tests/data/sequences_test_deinterleaved_1.fa
delete mode 100644 fastaq/tests/data/sequences_test_deinterleaved_2.fa
delete mode 100644 fastaq/tests/data/sequences_test_deinterleaved_bad2_1.fa
delete mode 100644 fastaq/tests/data/sequences_test_deinterleaved_bad2_2.fa
delete mode 100644 fastaq/tests/data/sequences_test_deinterleaved_bad_1.fa
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delete mode 100644 fastaq/tests/data/sequences_test_enumerate_names.fa
delete mode 100644 fastaq/tests/data/sequences_test_enumerate_names.fa.out.keep_suffix
delete mode 100644 fastaq/tests/data/sequences_test_enumerate_names.fa.out.start.1
delete mode 100644 fastaq/tests/data/sequences_test_enumerate_names.fa.out.start.1.rename_file
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delete mode 100644 fastaq/tests/data/sequences_test_extend_gaps.fa.out
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delete mode 100644 fastaq/tests/data/sequences_test_fai_test.fa.fai
delete mode 100644 fastaq/tests/data/sequences_test_fail_no_AT.fq
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delete mode 100644 fastaq/tests/data/sequences_test_fail_no_qual.fq
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delete mode 100644 fastaq/tests/data/sequences_test_fastaq_replace_bases.expected.fa
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delete mode 100644 fastaq/tests/data/sequences_test_filter_by_ids_file.fa.filtered.invert
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delete mode 100644 fastaq/tests/data/sequences_test_get_seqs_flanking_gaps.fa
delete mode 100644 fastaq/tests/data/sequences_test_get_seqs_flanking_gaps.fa.out
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delete mode 100644 fastaq/tests/data/sequences_test_gffv3.gff.fasta
delete mode 100644 fastaq/tests/data/sequences_test_gffv3.gff.to_fasta
delete mode 100644 fastaq/tests/data/sequences_test_gffv3.no_FASTA_line.gff
delete mode 100644 fastaq/tests/data/sequences_test_gffv3.no_FASTA_line.gff.to_fasta
delete mode 100644 fastaq/tests/data/sequences_test_gffv3.no_seq.2.gff
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delete mode 100644 fastaq/tests/data/sequences_test_good_file.fq.to_fasta
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delete mode 100644 fastaq/tests/data/sequences_test_interleaved_bad.fa
delete mode 100644 fastaq/tests/data/sequences_test_length_filter.fa
delete mode 100644 fastaq/tests/data/sequences_test_length_filter.min-0.max-1.fa
delete mode 100644 fastaq/tests/data/sequences_test_length_filter.min-0.max-inf.fa
delete mode 100644 fastaq/tests/data/sequences_test_length_filter.min-4.max-4.fa
delete mode 100644 fastaq/tests/data/sequences_test_make_random_contigs.default.fa
delete mode 100644 fastaq/tests/data/sequences_test_make_random_contigs.first-42.fa
delete mode 100644 fastaq/tests/data/sequences_test_make_random_contigs.name-by-letters.fa
delete mode 100644 fastaq/tests/data/sequences_test_make_random_contigs.prefix-p.fa
delete mode 100644 fastaq/tests/data/sequences_test_not_a_fastaq_file
delete mode 100644 fastaq/tests/data/sequences_test_one-per-line.fa
delete mode 100644 fastaq/tests/data/sequences_test_phylip.interleaved
delete mode 100644 fastaq/tests/data/sequences_test_phylip.interleaved.to_fasta
delete mode 100644 fastaq/tests/data/sequences_test_phylip.interleaved2
delete mode 100644 fastaq/tests/data/sequences_test_phylip.interleaved2.to_fasta
delete mode 100644 fastaq/tests/data/sequences_test_phylip.made_by_seaview
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delete mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.coords
delete mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.1
delete mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.2
delete mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.3
delete mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.4
delete mode 100644 fastaq/tests/data/sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.coords
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.2.1
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delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.2.3
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.2.4
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.3.1
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.3.2
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.3.3
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.4.1
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.4.2
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.4.3
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.6.1
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.6.2
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.6.limit2.1
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.6.limit2.2
delete mode 100644 fastaq/tests/data/sequences_test_split_test.fa.6.limit2.3
delete mode 100644 fastaq/tests/data/sequences_test_split_test.long.fa
delete mode 100644 fastaq/tests/data/sequences_test_split_test.long.fa.2.1
delete mode 100644 fastaq/tests/data/sequences_test_split_test.long.fa.2.2
delete mode 100644 fastaq/tests/data/sequences_test_strip_after_whitespace.fa
delete mode 100644 fastaq/tests/data/sequences_test_strip_after_whitespace.fa.to_fasta
delete mode 100644 fastaq/tests/data/sequences_test_strip_illumina_suffix.fq
delete mode 100644 fastaq/tests/data/sequences_test_strip_illumina_suffix.fq.stripped
delete mode 100644 fastaq/tests/data/sequences_test_to_unique_by_id.fa
delete mode 100644 fastaq/tests/data/sequences_test_to_unique_by_id.fa.out
delete mode 100644 fastaq/tests/data/sequences_test_translate.fa
delete mode 100644 fastaq/tests/data/sequences_test_translate.fa.frame0
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delete mode 100644 fastaq/tests/data/sequences_test_trim_Ns_at_end.fa
delete mode 100644 fastaq/tests/data/sequences_test_trim_Ns_at_end.fa.trimmed
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delete mode 100644 fastaq/tests/data/sequences_test_untrimmed.fq
delete mode 100644 fastaq/tests/data/utils_test_file_transpose.txt
delete mode 100644 fastaq/tests/data/utils_test_file_transposed.txt
delete mode 100644 fastaq/tests/data/utils_test_not_really_zipped.gz
delete mode 100644 fastaq/tests/data/utils_test_scaffolds.fa
delete mode 100644 fastaq/tests/data/utils_test_scaffolds.fa.to_contigs.fa
delete mode 100644 fastaq/tests/data/utils_test_scaffolds.fa.to_contigs.number_contigs.fa
delete mode 100644 fastaq/tests/data/utils_test_system_call.txt
delete mode 100644 fastaq/tests/intervals_test.py
delete mode 100644 fastaq/tests/sequences_test.py
delete mode 100644 fastaq/tests/tasks_test.py
delete mode 100644 fastaq/tests/utils_test.py
delete mode 100644 fastaq/utils.py
rename {scripts => src}/fastaq_capillary_to_pairs (100%)
rename {scripts => src}/fastaq_chunker (100%)
rename {scripts => src}/fastaq_count_sequences (100%)
rename {scripts => src}/fastaq_deinterleave (100%)
rename {scripts => src}/fastaq_enumerate_names (100%)
rename {scripts => src}/fastaq_extend_gaps (100%)
rename {scripts => src}/fastaq_fasta_to_fastq (100%)
rename {scripts => src}/fastaq_filter (100%)
rename {scripts => src}/fastaq_get_ids (100%)
rename {scripts => src}/fastaq_get_seq_flanking_gaps (100%)
rename {scripts => src}/fastaq_insert_or_delete_bases (100%)
rename {scripts => src}/fastaq_interleave (100%)
rename {scripts => src}/fastaq_make_random_contigs (100%)
rename {scripts => src}/fastaq_replace_bases (100%)
rename {scripts => src}/fastaq_reverse_complement (100%)
rename {scripts => src}/fastaq_scaffolds_to_contigs (100%)
rename {scripts => src}/fastaq_search_for_seq (100%)
rename {scripts => src}/fastaq_split_by_base_count (100%)
rename {scripts => src}/fastaq_strip_illumina_suffix (100%)
rename {scripts => src}/fastaq_to_fasta (100%)
rename {scripts => src}/fastaq_to_mira_xml (100%)
rename {scripts => src}/fastaq_to_perfect_reads (100%)
rename {scripts => src}/fastaq_to_quasr_primers_file (100%)
rename {scripts => src}/fastaq_to_random_subset (100%)
rename {scripts => src}/fastaq_to_tiling_bam (100%)
rename {scripts => src}/fastaq_to_unique_by_id (100%)
rename {scripts => src}/fastaq_translate (100%)
rename {scripts => src}/fastaq_trim_Ns_at_end (100%)
rename {scripts => src}/fastaq_trim_ends (100%)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git
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