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Merge pull request #41 from bcgsc/tigmint-long-bugs
Fix barcode naming bug
2 parents 4c9ebff + 2f63995 commit 929a588

17 files changed

+168
-66
lines changed

README.md

+3-3
Original file line numberDiff line numberDiff line change
@@ -121,7 +121,7 @@ tigmint-make metrics draft=myassembly reads=myreads ref=GRCh38 G=3088269832
121121
To run Tigmint with long reads in fasta or fastq format (`reads.fa.gz` or `reads.fq.gz`) on the draft assembly `draft.fa`:
122122

123123
```sh
124-
tigmint-make tigmint-long draft=myassembly reads=myreads span=auto gsize=genomesize
124+
tigmint-make tigmint-long draft=myassembly reads=myreads span=auto G=genomesize
125125
```
126126

127127
- `minimap2 map-ont` is used to align long reads from the Oxford Nanopore Technologies (ONT) platform, which is the default input for Tigmint. To use PacBio long reads specify the parameter `longmap=pb`
@@ -131,7 +131,7 @@ tigmint-make tigmint-long draft=myassembly reads=myreads span=auto gsize=genomes
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132132
+ `tigmint-make` is a Makefile script, and so any `make` options may also be used with `tigmint-make`, such as `-n` (`--dry-run`).
133133
+ The file extension of the assembly must be `.fa` and the reads `.fq.gz` (or `.fa.gz` for long reads), and the extension is not included in the parameters `draft` and `reads`. These specific file name requirements result from implementing the pipeline in GNU Make.
134-
+ The minimum spanning molecules parameter (`span`) for `tigmint-cut` is heavily dependent on the sequence coverage of the linked or long reads provided. When running Tigmint with long reads, use `span=auto` and set `gsize` to your assembly organism's haploid genome size for this parameter to be calculated automatically, or explicitly set `span` to a specific number if you are interested in adjusting it. See [Tips](https://github.com/bcgsc/tigmint/tree/long-to-linked/#Note) for more details.
134+
+ The minimum spanning molecules parameter (`span`) for `tigmint-cut` is heavily dependent on the sequence coverage of the linked or long reads provided. When running Tigmint with long reads, use `span=auto` and set `G` to your assembly organism's haploid genome size for this parameter to be calculated automatically, or explicitly set `span` to a specific number if you are interested in adjusting it. See [Tips](https://github.com/bcgsc/tigmint/tree/long-to-linked/#Note) for more details.
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136136
# tigmint-make commands
137137

@@ -178,7 +178,7 @@ tigmint-make tigmint-long draft=myassembly reads=myreads span=auto gsize=genomes
178178
- Sort by BX tag using `samtools sort -tBX`.
179179
- Merge multiple BAM files using `samtools merge -tBX`.
180180
- When aligning long reads with Minimap2, use the `-y` option to include the barcode in the BX tag of the alignments.
181-
- When using long reads, the minimum spanning molecule thresholds (`span`) should be no greater than 1/4 of the sequence coverage. Setting the parameter `span=auto` allows the appropriate parameter value to be selected automatically (this setting requires the parameter `gsize` as well).
181+
- When using long reads, the minimum spanning molecule thresholds (`span`) should be no greater than 1/4 of the sequence coverage. Setting the parameter `span=auto` allows the appropriate parameter value to be selected automatically (this setting requires the parameter `G` as well).
182182
- When using long reads, the edit distance threshold (`nm`) is automatically set to the cut length (`cut`) to compensate for the higher error rate and length. This parameter should be kept relatively high to include as many alignments as possible.
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184184
# Using stLFR linked reads

azure-pipelines.yml

+2-1
Original file line numberDiff line numberDiff line change
@@ -27,7 +27,8 @@ jobs:
2727
echo path:
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echo $PATH
2929
sudo /home/linuxbrew/.linuxbrew/bin/pip3 install pytest
30-
sudo HOMEBREW_NO_AUTOUPDATE=1 /home/linuxbrew/.linuxbrew/bin/brew install bedtools bwa samtools gnu-time
30+
sudo HOMEBREW_NO_AUTOUPDATE=1 /home/linuxbrew/.linuxbrew/bin/brew tap brewsci/bio
31+
sudo HOMEBREW_NO_AUTOUPDATE=1 /home/linuxbrew/.linuxbrew/bin/brew install bedtools bwa samtools gnu-time minimap2
3132
cd tests/
3233
pytest -vs tigmint_test.py
3334
env:

bin/long-to-linked

+4-2
Original file line numberDiff line numberDiff line change
@@ -23,15 +23,17 @@ def cut_reads(length, min_size, auto_span, genome_size, span_out):
2323
total_bases = 0
2424

2525
with open("/dev/stdin", 'rt') as reads:
26+
barcode = 0
2627
if not reads.isatty(): # Check that reads are being piped in from stdin
2728
for header, seq, _, _ in read_fasta(reads):
2829
read_length = len(seq)
2930
total_bases += read_length
3031
if read_length >= min_size:
3132
split_reads = split_long_read(seq, length)
3233
for i, read in enumerate(split_reads):
33-
print(">" + header + "_" + str(i) + " BX:Z:" + str(i), file=sys.stdout)
34+
print(">" + header + "_" + str(i) + " BX:Z:" + str(barcode), file=sys.stdout)
3435
print(read, file=sys.stdout)
36+
barcode += 1
3537
if auto_span:
3638
with open(span_out, "w") as span_file:
3739
span = int(total_bases / genome_size * cov_to_span)
@@ -46,7 +48,7 @@ def main():
4648
parser = argparse.ArgumentParser(description="Segment long reads into short reads and calculate span.")
4749
parser.add_argument("-v", "--version",
4850
action="version",
49-
version="long-to-linked 1.2.0")
51+
version="long-to-linked 1.2.1")
5052
parser.add_argument("-l", "--length",
5153
type=int,
5254
default=500,

bin/tigmint-cut

+1-1
Original file line numberDiff line numberDiff line change
@@ -238,7 +238,7 @@ def get_span(filename):
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239239
def main():
240240
parser = argparse.ArgumentParser(description="Find misassembled regions in assembly using Chromium molecule extents")
241-
parser.add_argument("--version", action="version", version="tigmint-cut 1.2.0")
241+
parser.add_argument("--version", action="version", version="tigmint-cut 1.2.1")
242242
parser.add_argument("fasta", type=str, help="Reference genome fasta file (must have FAI index generated)")
243243
parser.add_argument("bed", type=str, help="Sorted bed file of molecule extents")
244244
parser.add_argument("-o", "--fastaout", type=str, help="The output FASTA file.", required=True)

bin/tigmint-make

+1-1
Original file line numberDiff line numberDiff line change
@@ -123,7 +123,7 @@ help:
123123
@echo 'For more information see https://bcgsc.github.io/tigmint/'
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125125
version:
126-
@echo "Tigmint 1.2.0"
126+
@echo "Tigmint 1.2.1"
127127
@echo "Written by Shaun Jackman @sjackman."
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129129
all: tigmint arcs

bin/tigmint-molecule

+1-1
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@@ -230,7 +230,7 @@ class MolecIdentifier:
230230
"Read a SAM/BAM file and output a TSV file. "
231231
"The SAM/BAM file must be sorted by BX tag and then by position.")
232232
parser.add_argument(
233-
'--version', action='version', version='tigmint-molecule 1.2.0')
233+
'--version', action='version', version='tigmint-molecule 1.2.1')
234234
parser.add_argument(
235235
metavar="BAM", dest="in_bam_filename",
236236
help="Input BAM file sorted by BX tag then position, - for stdin")

setup.py

+1-1
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@@ -5,7 +5,7 @@
55

66
setuptools.setup(
77
name="tigmint",
8-
version="1.2.0",
8+
version="1.2.1",
99
author="Shaun Jackman",
1010
author_email="[email protected]",
1111
description="Correct misassemblies using linked or long reads",
File renamed without changes.
File renamed without changes.
Original file line numberDiff line numberDiff line change
@@ -1,26 +1,24 @@
1-
test 0 4998 14 4
2-
test 3 4998 2 7
3-
test 4 4003 16 6
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test 58 3827 26 5
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test 80 4998 7 5
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test 169 4737 8 5
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test 306 3950 31 5
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test 348 4993 13 5
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test 393 4993 1 9
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test 398 4067 11 6
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test 434 4998 0 8
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test 478 4998 18 6
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test 556 4995 21 6
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test 590 4874 6 4
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test 856 4994 12 7
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test 859 4998 29 6
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test 987 3538 10 4
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test 1004 3993 19 5
19-
test 1057 4993 22 5
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test 1126 4614 5 5
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test 1142 4776 15 4
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test 1583 4510 20 5
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test 1634 4997 4 6
24-
test 1998 4632 3 6
25-
test 2685 4998 23 5
26-
test 2687 4788 24 4
1+
test 0 2393 13 5
2+
test 4 2453 31 5
3+
test 4 2607 294 5
4+
test 6 2186 21 4
5+
test 80 2149 48 4
6+
test 169 2624 7 4
7+
test 479 2585 35 4
8+
test 2685 4993 11 5
9+
test 2685 4994 36 6
10+
test 2685 4998 140 6
11+
test 2685 4998 16 6
12+
test 2685 4998 18 5
13+
test 2685 4998 46 6
14+
test 2686 4995 256 5
15+
test 2686 4997 26 5
16+
test 2686 4998 10 5
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test 2687 4993 6 5
18+
test 2689 4998 30 5
19+
test 2700 4776 38 4
20+
test 2717 4737 14 4
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test 2735 4874 45 5
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test 2786 4788 55 4
23+
test 2800 4829 51 4
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test 2912 4998 27 4
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,6 @@
1-
>test
2-
TTTAAAAACGTGCAAGCGCGCTCCATCGAACAAATCCAATTGGCGGTAATTCAAATAGGAATTAGGCAAAGACTGAGATTTTTTCAATTTTCAAAAAAAATCATATAAAATTTAGAAAATTTTTTTGTATGTTTTAATCATGATATTTGGTCATTGTGGTTACCATAGGCGTGTTTTAAAGCAATTTCCCCAATGGCGCTACTCCACCTTTAAGTTGAAAATGCACTGAAAATCCATTTTCGCACCGAAAAATTCGCATTTTCCTATAAAAATTCTGCAAAAGCCGAAAAAAAACGCGAAAAATTCAATATTCTTTGATTTTTTTTTAATGAAAATGAGCTAAAAAGCTAATTTTTCCCATTTTTTCAGGAAAGAAATCCGTGTTTTGCTTTTAAACATTTTTTATAGGAAAATTGTCGAAAAATGCAGTTTTCTCGACAATTTTTTTGCCACGGTTACTGTGACTTTTATTTTCGGCGAAATTTTCAAAATTACAGAAGGTTTTGATTTATAAATAAATCTATAAGAATTTTTTTGTTAAAAAACTTCCAGTTGAAAACCAATAATTTTCTCCAATTTTTCCAGACGTAGTCGCCTCATTCTCAAAAATTGGTGATAGTTTTGAACGAATTGCACGTGGAGAACCGAATAAATCATTGGCACGTACATTTGCACAGGGAGCCGACGCCATGTTTAAGCTCAAGAAGGTAATGCTGGAAATTTTTCCGAATTTTTGGGTTACTGTAAGCTACAGTATCCCTCGCTAAATTCAAAAACTCAAAACTCAAATTCCAGCAATTTGGGACGAAAAAAATGCGGAAAATCTGATTTTTTACATTTTTTTTGTGATTTTCAGTGAAAATTTCAGATTTTTAATTAGAAAATTGATTTTTTTTCACATTTTCTGAAATTTTCATTTTCTTTTTTTTTGGGTTACTGTAGGCTACAGTATCCCTCGCTAAATTCAAAAACTCGGAGTTTCAGTTATTTTTTTGGGCGAAAAAAGTTTTCGAAATTTGTAACAAAGTTTATTCGACTCAAAATTGTCTGAAAACACTGAATTTCTGAATGAAAATTCTCAACAAAAAAAAAGAGTTATAGCGGCTCAAAAAATGACCTAAAATTAGTTTAAAGTTTGAAATTTGACTTGTTAGCGGCTGGAACCTAACTTTTTTGAAATCACCGTCTAATTTTGGGTATACAAGTTTATTATCATGCATTTTCAATTCGATTTGGGTACATTTAAGGTCAAATCTCCCATCGGCCTTAAATGTACCCAAATTGAGTTGAAAATGCATGATAATTAACCTGTAAACCAAAACTTAGACGGTGATTTCAAAAAAAGTAAGTATCGAGCCGCTAACAAGTTAAATTTCAAACTTTAAACTAATTTTATGTCATTTTTTGAGCCGCTATAACTCTTTTTTTTGAGAATTTTCATTATGAAATTCGGTGTTTTCAGAGACAATTTTGAGTCTAATAAACTTTTGTTACAAATTTCGAAAACTTTTTTCGCCCAAAAAAAAACTGAAACTCCAAGTTTTTGAATTTTGCGAGGGATACTGTAGCCTACTACAGTAACCCAAAAAAAAAAGAAGGTGAAAATTTCAGAAAATGTGAAAAAAAAAATCAATTTTCTAATTAAAAATCTGAAATTTTCCCTGAAAATCCCAAAAAAAAAAAAAAAAACAAAAAAGATTTTCCGCATTTTTTTTTCGTCCCAAATTGCTGGAATTTGAGTTTTGCACGATTTTTGTGCATTTTTCTTGAAAAAAAAAACGCAAAAATCGCCTTGAAACTCGAAATTTCGATTTTTTCGAAAATTCTCAATTTTCGTCGTTTTTTTTTAAATGAAAAAAAAAACAAAAAAGGAATGCAATTTTTGCTTTAAAAAAATTTAATTTGAAAACTGGAAAAATTGAATTTTCCAATGAAATTTCTGAAAAAAAGTGTGAAATTTCGATTTTCCAACAGAGGAAGGAATCCAATTTTTGCAATTTTTGCTAGGAAATTTTAATTTGAAAACTGGAAAAATTGGGTTTTTTTTTTCGACAAAACGTTGTCGTTTCCCTCAAAATATCGAAGAAATATAGTATAAAAACTACGAAATTCCGCTTTTTCAATGTGAAAAATGCCAAAAATTGCACATTTTCAGCCCGAAAACCTTCTAAATCACCTATTTTTTTTGCAGGTAGAATCCCGTTCATCAAACGATGAAGAGCTTAAATTGGGCGATACACTTCACTATTTTGCACGTGATACACAGGCTGCAAAGGATCTTTTGTATCGGAGAATGAGATGTTTGGCAAATTACGAAGCAGCGAATAAGAATTTGGAACGAGCTCGAGCCAAAAATCGAGAAATTCCAAAGGTTTATTAAATTCTGAGCTCAAAATCACACTCACTGCAACTTTTTCCTCACGAGGGACGAGGAAAAGTGGTTTCTAGGCCATGGCCGAGGGGTCGACAAGTTTCAGCGGCCATTTATCTTGCTTTGTTTTCCGCCTGTTTTCTTTCGTTTTTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGATAAATAAATATTTTTGCAGATGCTAAAACAATTTCCAAGTAAAAAAATTATGTATTCAGTGGGCAAGCAGCGGTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATTTTTTGGACGGATTTTTTTCCAAACTTTTGTCGTTTTCTAATAATGTGTTCTAAACAAAGAAAAATCCACACACAAACATCAATTCAAAGCTGAAAAGAAGCGAGATCTGAAAAATGCCTGAAAAAATAGGCTCCGAGTTAGGACACTTGGGGTGGTCAACAACTTTTGTGACTATTGTCAAATGAAAGATCATAATTGATAACATGAATYCCCAAAGTTTCATAAAAATCGATTTGCAGCGAACAAAGTTATGATTTTTGACCCGGAACTTATTTGgaGACCTAATAGTAATCGTATTAAAAATCGAATTTTTTCAAAATTTCGAAAAAAAAGTTTTTTTTTTTTTAATTTTTGAAAATTTCCAAAGCATCATTGAACACTAGTCGGTTATATTTTTAATATTCAAAATAATTTTTTTTTTGAGAAATATTAGAAATTATCAATGGTTTTTCGAAAAAAACATTTTTTTTTGGAAAATTTGTATATTCCCATTACTAATGCAATAATCGTATTGAAACTCATTTTGTTTTAATTCAAAATTTTTTTAAGGAAATAGGTTTTATTGTCATTACTTATGCAATGATTGTATTAAAAATCAACTTTTTCTTGAAATTTCGAAAAAAAAATTTTGAAAAATTTTGAAAAATTTTGAAGCATCATTAAATAAACACTGGTGGGTTATATTTTTAATACTCAAAAAATGTTTATTTTAAAAAAAAGCCTATAGTATTAAATATCGATTTTTGAAAAAAATTATAAAAAACATTTTAAATTCTAAAGTTTTAAGCACGTACTCGGAGTGTTTTCCAAAAAATAAAGTAATTTAATTGAATTTTTTTTTTTGGAAATATTTAAATTTATCTATGATTTTTGGTGTTTAACAAGTGGGAAGAGTTTTTCGAAAAAAAAAAATTTTTTTTTGGAAAATTTGTATATTCCCATTACTAATGCAATAATCGTATTGAAACTCAATTTGTTTTAATTCAAAATTTTTTTTAGGTAAATAGGTTTAATGTCATTACATATGCAATGATTGTATTAAAAATCGACTTTTTCTTGAAATTGCGAAAAAATATTTTTTCGGAAAATTTGTGTATTTCCATTACTTATGCAATAATAGTATTTAAAATAAATGTTTTTTTAATTCAAAAAATTTTTTTTTGGAAGATTGATATATTCCCATTATTTATGCAATAATCGTATGGGAAATCGATTTTTTTATTTAAAATTTTTTTTGTAAATTTTGTAATTTTACTGATTTTTTGTTAATTTTTAATTTCCTTACCTATGTGCTCCAGTCTCATCACAAATGTCACCTTTCGCATAGATTTGACTAATCTGATCAATTTGATTGTTTCCCTGAAATCATTATTCACTTATATAAGATAACTCTATTATGGCGGGAACACAAAATCTCTGAAAATGCGTATTGCACAACATATTTGACGCGCAAAATATCTCGTAGCGAAAACTACTGTAGCTCTTGTGTCGATTTACGACGGGCTTGATTCTCGGAAAAAAACCGAATTTTTCGCGAATTTTGACACCGATATTCAATTTTTCTCCGTTTTTTTTTTCTTATTCCTTGGTCTTATTTGTGATCTTTATTTTAATACTTTATCCATTAATAAATTAATTTAATTGAAAAACGTCTAATATAGGCGCTATTATGATGAGTAAACTCCTACATGCGTATTTTTACATTATTTCCCGCCTATTACGGTTTAAAAAAACGCTTGTGGGAGTATTATCTTCAAAATTACGATAATATTGGGCATTTTTCAATTAAATTAATATTTACTAATGGATAAAATATTAAAATTAAGCACAAATAAAAAACCAAGGAATCTGGAAAAAAAAACGACGAAGAAAAATTAAATATCGCTGTCGAAATTCGAAAAATTTGGTTTTTTTTCCGAGAATCAAGCCGACGTAAATCGACACGAGCGCTACAGTAGTTTTCGCTCACTGCAACTTTTTCCTCACGAGGGACGAGGAAAAGTGGTTTGTTCTTTCGTTTTTCACAGCTTTTTCTCGTTTTTTCTTATTAAAACTGATAAACAAATATTTTTTGCAGATGCCAAAACGATTTCCAAGTCAAAAAAATTATGTATTCAGTGGGCAAGCAGCGGTGAAAGTGGTCAATGTAAAATGATGGATTACGGGAATACAAAACCTAAACTTTTTCTGAAACATGATACATATGTTGCTTAAATGCTGAAATTACCTGGTTTTCATAGCGAGACCGCTGAAAAAGTTTTGAGGTTTTCAAAATTCAACTTTTTGTGCGAAAATCTCGACTTTTTCACC
1+
>test-1
2+
TTTAAAAACGTGCAAGCGCGCTCCATCGAACAAATCCAATTGGCGGTAATTCAAATAGGAATTAGGCAAAGACTGAGATTTTTTCAATTTTCAAAAAAAATCATATAAAATTTAGAAAATTTTTTTGTATGTTTTAATCATGATATTTGGTCATTGTGGTTACCATAGGCGTGTTTTAAAGCAATTTCCCCAATGGCGCTACTCCACCTTTAAGTTGAAAATGCACTGAAAATCCATTTTCGCACCGAAAAATTCGCATTTTCCTATAAAAATTCTGCAAAAGCCGAAAAAAAACGCGAAAAATTCAATATTCTTTGATTTTTTTTTAATGAAAATGAGCTAAAAAGCTAATTTTTCCCATTTTTTCAGGAAAGAAATCCGTGTTTTGCTTTTAAACATTTTTTATAGGAAAATTGTCGAAAAATGCAGTTTTCTCGACAATTTTTTTGCCACGGTTACTGTGACTTTTATTTTCGGCGAAATTTTCAAAATTACAGAAGGTTTTGATTTATAAATAAATCTATAAGAATTTTTTTGTTAAAAAACTTCCAGTTGAAAACCAATAATTTTCTCCAATTTTTCCAGACGTAGTCGCCTCATTCTCAAAAATTGGTGATAGTTTTGAACGAATTGCACGTGGAGAACCGAATAAATCATTGGCACGTACATTTGCACAGGGAGCCGACGCCATGTTTAAGCTCAAGAAGGTAATGCTGGAAATTTTTCCGAATTTTTGGGTTACTGTAAGCTACAGTATCCCTCGCTAAATTCAAAAACTCAAAACTCAAATTCCAGCAATTTGGGACGAAAAAAATGCGGAAAATCTGATTTTTTACATTTTTTTTGTGATTTTCAGTGAAAATTTCAGATTTTTAATTAGAAAATTGATTTTTTTTCACATTTTCTGAAATTTTCATTTTCTTTTTTTTTGGGTTACTGTAGGCTACAGTATCCCTCGCTAAATTCAAAAACTCGGAGTTTCAGTTATTTTTTTGGGCGAAAAAAGTTTTCGAAATTTGTAACAAAGTTTATTCGACTCAAAATTGTCTGAAAACACTGAATTTCTGAATGAAAATTCTCAACAAAAAAAAAGAGTTATAGCGGCTCAAAAAATGACCTAAAATTAGTTTAAAGTTTGAAATTTGACTTGTTAGCGGCTGGAACCTAACTTTTTTGAAATCACCGTCTAATTTTGGGTATACAAGTTTATTATCATGCATTTTCAATTCGATTTGGGTACATTTAAGGTCAAATCTCCCATCGGCCTTAAATGTACCCAAATTGAGTTGAAAATGCATGATAATTAACCTGTAAACCAAAACTTAGACGGTGATTTCAAAAAAAGTAAGTATCGAGCCGCTAACAAGTTAAATTTCAAACTTTAAACTAATTTTATGTCATTTTTTGAGCCGCTATAACTCTTTTTTTTGAGAATTTTCATTATGAAATTCGGTGTTTTCAGAGACAATTTTGAGTCTAATAAACTTTTGTTACAAATTTCGAAAACTTTTTTCGCCCAAAAAAAAACTGAAACTCCAAGTTTTTGAATTTTGCGAGGGATACTGTAGCCTACTACAGTAACCCAAAAAAAAAAGAAGGTGAAAATTTCAGAAAATGTGAAAAAAAAAATCAATTTTCTAATTAAAAATCTGAAATTTTCCCTGAAAATCCCAAAAAAAAAAAAAAAAACAAAAAAGATTTTCCGCATTTTTTTTTCGTCCCAAATTGCTGGAATTTGAGTTTTGCACGATTTTTGTGCATTTTTCTTGAAAAAAAAAACGCAAAAATCGCCTTGAAACTCGAAATTTCGATTTTTTCGAAAATTCTCAATTTTCGTCGTTTTTTTTTAAATGAAAAAAAAAACAAAAAAGGAATGCAATTTTTGCTTTAAAAAAATTTAATTTGAAAACTGGAAAAATTGAATTTTCCAATGAAATTTCTGAAAAAAAGTGTGAAATTTCGATTTTCCAACAGAGGAAGGAATCCAATTTTTGCAATTTTTGCTAGGAAATTTTAATTTGAAAACTGGAAAAATTGGGTTTTTTTTTTCGACAAAACGTTGTCGTTTCCCTCAAAATATCGAAGAAATATAGTATAAAAACTACGAAATTCCGCTTTTTCAATGTGAAAAATGCCAAAAATTGCACATTTTCAGCCCGAAAACCTTCTAAATCACCTATTTTTTTTGCAGGTAGAATCCCGTTCATCAAACGATGAAGAGCTTAAATTGGGCGATACACTTCACTATTTTGCACGTGATACACAGGCTGCAAAGGATCTTTTGTATCGGAGAATGAGATGTTTGGCAAATTACGAAGCAGCGAATAAGAATTTGGAACGAGCTCGAGCCAAAAATCGAGAAATTCCAAAGGTTTATTAAATTCTGAGCTCAAAATCACACTCACTGCAACTTTTTCCTCACGAGGGACGAGGAAAAGTGGTTTCTAGGCCATGGCCGAGGGGTCGACAAGTTTCAGCGGCCATTTATCTTGCTTTGTTTTCCGCCTGTTTTCTTTCGTTTTTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGATAAATAAATATTTTTGCAGATGCTAAAACAATTTCCAAGTAAAAAAA
3+
>test-2
4+
TTATGTATTCAGTGGGCAAGCAGCGGTG
5+
>test-3
6+
ATTTTTTGGACGGATTTTTTTCCAAACTTTTGTCGTTTTCTAATAATGTGTTCTAAACAAAGAAAAATCCACACACAAACATCAATTCAAAGCTGAAAAGAAGCGAGATCTGAAAAATGCCTGAAAAAATAGGCTCCGAGTTAGGACACTTGGGGTGGTCAACAACTTTTGTGACTATTGTCAAATGAAAGATCATAATTGATAACATGAATYCCCAAAGTTTCATAAAAATCGATTTGCAGCGAACAAAGTTATGATTTTTGACCCGGAACTTATTTGgaGACCTAATAGTAATCGTATTAAAAATCGAATTTTTTCAAAATTTCGAAAAAAAAGTTTTTTTTTTTTTAATTTTTGAAAATTTCCAAAGCATCATTGAACACTAGTCGGTTATATTTTTAATATTCAAAATAATTTTTTTTTTGAGAAATATTAGAAATTATCAATGGTTTTTCGAAAAAAACATTTTTTTTTGGAAAATTTGTATATTCCCATTACTAATGCAATAATCGTATTGAAACTCATTTTGTTTTAATTCAAAATTTTTTTAAGGAAATAGGTTTTATTGTCATTACTTATGCAATGATTGTATTAAAAATCAACTTTTTCTTGAAATTTCGAAAAAAAAATTTTGAAAAATTTTGAAAAATTTTGAAGCATCATTAAATAAACACTGGTGGGTTATATTTTTAATACTCAAAAAATGTTTATTTTAAAAAAAAGCCTATAGTATTAAATATCGATTTTTGAAAAAAATTATAAAAAACATTTTAAATTCTAAAGTTTTAAGCACGTACTCGGAGTGTTTTCCAAAAAATAAAGTAATTTAATTGAATTTTTTTTTTTGGAAATATTTAAATTTATCTATGATTTTTGGTGTTTAACAAGTGGGAAGAGTTTTTCGAAAAAAAAAAATTTTTTTTTGGAAAATTTGTATATTCCCATTACTAATGCAATAATCGTATTGAAACTCAATTTGTTTTAATTCAAAATTTTTTTTAGGTAAATAGGTTTAATGTCATTACATATGCAATGATTGTATTAAAAATCGACTTTTTCTTGAAATTGCGAAAAAATATTTTTTCGGAAAATTTGTGTATTTCCATTACTTATGCAATAATAGTATTTAAAATAAATGTTTTTTTAATTCAAAAAATTTTTTTTTGGAAGATTGATATATTCCCATTATTTATGCAATAATCGTATGGGAAATCGATTTTTTTATTTAAAATTTTTTTTGTAAATTTTGTAATTTTACTGATTTTTTGTTAATTTTTAATTTCCTTACCTATGTGCTCCAGTCTCATCACAAATGTCACCTTTCGCATAGATTTGACTAATCTGATCAATTTGATTGTTTCCCTGAAATCATTATTCACTTATATAAGATAACTCTATTATGGCGGGAACACAAAATCTCTGAAAATGCGTATTGCACAACATATTTGACGCGCAAAATATCTCGTAGCGAAAACTACTGTAGCTCTTGTGTCGATTTACGACGGGCTTGATTCTCGGAAAAAAACCGAATTTTTCGCGAATTTTGACACCGATATTCAATTTTTCTCCGTTTTTTTTTTCTTATTCCTTGGTCTTATTTGTGATCTTTATTTTAATACTTTATCCATTAATAAATTAATTTAATTGAAAAACGTCTAATATAGGCGCTATTATGATGAGTAAACTCCTACATGCGTATTTTTACATTATTTCCCGCCTATTACGGTTTAAAAAAACGCTTGTGGGAGTATTATCTTCAAAATTACGATAATATTGGGCATTTTTCAATTAAATTAATATTTACTAATGGATAAAATATTAAAATTAAGCACAAATAAAAAACCAAGGAATCTGGAAAAAAAAACGACGAAGAAAAATTAAATATCGCTGTCGAAATTCGAAAAATTTGGTTTTTTTTCCGAGAATCAAGCCGACGTAAATCGACACGAGCGCTACAGTAGTTTTCGCTCACTGCAACTTTTTCCTCACGAGGGACGAGGAAAAGTGGTTTGTTCTTTCGTTTTTCACAGCTTTTTCTCGTTTTTTCTTATTAAAACTGATAAACAAATATTTTTTGCAGATGCCAAAACGATTTCCAAGTCAAAAAAATTATGTATTCAGTGGGCAAGCAGCGGTGAAAGTGGTCAATGTAAAATGATGGATTACGGGAATACAAAACCTAAACTTTTTCTGAAACATGATACATATGTTGCTTAAATGCTGAAATTACCTGGTTTTCATAGCGAGACCGCTGAAAAAGTTTTGAGGTTTTCAAAATTCAACTTTTTGTGCGAAAATCTCGACTTTTTCACC
Original file line numberDiff line numberDiff line change
@@ -1 +1,3 @@
1-
test 0 4998 test
1+
test 0 2607 test-1
2+
test 2607 2685 test-2
3+
test 2685 4998 test-3
Binary file not shown.
+1-3
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@@ -1,13 +1,11 @@
11
#!/bin/bash
22

3-
set -eux
4-
53
echo "Running tigmint with linked reads..."
64

75
../../bin/tigmint-make tigmint draft=test_contig reads=test_linkedreads
86

97
echo "Running tigmint with long reads..."
108

11-
../../bin/tigmint-make tigmint-long draft=test_contig_long reads=test_longreads span=auto gsize=1000000
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../../bin/tigmint-make tigmint-long draft=test_contig_long reads=test_longreads span=auto G=1000000
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echo "Done! Compare your output files to those in the 'expected_outputs' directory to ensure that the run was successful."

tests/test_longreads.cut500.fa.gz

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