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allow alignment file indices with name pattern {filename}.{bai/crai} #112

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Merged
ryanlayer merged 3 commits into from
Sep 5, 2020
Merged

allow alignment file indices with name pattern {filename}.{bai/crai} #112

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280a95d
added support for alignment file indices in the {filename}.bai style …
jbelyeu Sep 4, 2020
25466bd
Merge remote-tracking branch 'upstream/master' into master
jbelyeu Sep 4, 2020
0b2e59b
Update README.md
jbelyeu Sep 4, 2020
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3 changes: 1 addition & 2 deletions README.md
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Expand Up @@ -117,8 +117,7 @@ conda install -c bioconda samplot
## Examples:

Samplot requires either BAM files or CRAM files as primary input. If you use
CRAM, you'll also need a reference genome like one used the the [1000 Genomes
Project](ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz).
CRAM, you'll also need a reference genome. You can easily acquire a reference genome file with [GGD](https://github.com/gogetdata/ggd-cli), which is also available from conda.

### Basic use case
Using data from NA12878, NA12889, and NA12890 in the
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2 changes: 1 addition & 1 deletion samplot/__init__.py
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@@ -1,2 +1,2 @@
#!/usr/bin/env python
__version__ = "1.0.17"
__version__ = "1.0.18"
4 changes: 3 additions & 1 deletion samplot/samplot.py
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Expand Up @@ -2106,7 +2106,9 @@ def bam_file(bam):
parser.error("alignment file {} is not in SAM/BAM/CRAM format".format(bam))
idx_type = idx_options[options.index(ext)]
#try the type-specific index name
if not os.path.isfile(bam + "." + idx_type):
picard_bam = os.path.splitext(bam)[0]
if (not os.path.isfile(bam + "." + idx_type) and
not os.path.isfile(picard_bam + "." + idx_type)):
idx_type = idx_options[3]
#try the csi index name
if not os.path.isfile(bam + "." + idx_type):
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