Check command return status

[adthrasher]

pipeline/utils.py

Line 1115 in 8108e90

command = '%s view %s %s' % (samtoolsString,self._bam,locusLine)

All of these shell-outs need to check the return status of the command. For example running with the following feature:

chrM	ENSEMBL	transcript	1	2577	.	+	.	transcript_id=ENST00000387314.1

Yields all 0s in the coverage bins.

GENE_ID	locusLine	bin_1_test.bam	bin_2_test.bam	bin_3_test.bam	bin_4_test.bam	bin_5_test.bam	bin_6_test.bam	bin_7_test.bam	bin_8_test.bam	bin_9_test.bam	bin_10_test.bam	bin_11_test.bam	bin_12_test.bam	bin_13_test.bam	bin_14_test.bam	bin_15_test.bam	bin_16_test.bam	bin_17_test.bam	bin_18_test.bam	bin_19_test.bam	bin_20_test.bam	bin_21_test.bam	bin_22_test.bam	bin_23_test.bam	bin_24_test.bam	bin_25_test.bam	bin_26_test.bam	bin_27_test.bam	bin_28_test.bam	bin_29_test.bam	bin_30_test.bam	bin_31_test.bam	bin_32_test.bam	bin_33_test.bam	bin_34_test.bam	bin_35_test.bam	bin_36_test.bam	bin_37_test.bam	bin_38_test.bam	bin_39_test.bam	bin_40_test.bam	bin_41_test.bam	bin_42_test.bam	bin_43_test.bam	bin_44_test.bam	bin_45_test.bam	bin_46_test.bam	bin_47_test.bam	bin_48_test.bam	bin_49_test.bam	bin_50_test.bam	bin_51_test.bam	bin_52_test.bam	bin_53_test.bam	bin_54_test.bam	bin_55_test.bam	bin_56_test.bam	bin_57_test.bam	bin_58_test.bam	bin_59_test.bam	bin_60_test.bam	bin_61_test.bam	bin_62_test.bam	bin_63_test.bam	bin_64_test.bam	bin_65_test.bam	bin_66_test.bam	bin_67_test.bam	bin_68_test.bam	bin_69_test.bam	bin_70_test.bam	bin_71_test.bam	bin_72_test.bam	bin_73_test.bam	bin_74_test.bam	bin_75_test.bam	bin_76_test.bam	bin_77_test.bam	bin_78_test.bam	bin_79_test.bam	bin_80_test.bam	bin_81_test.bam	bin_82_test.bam	bin_83_test.bam	bin_84_test.bam	bin_85_test.bam	bin_86_test.bam	bin_87_test.bam	bin_88_test.bam	bin_89_test.bam	bin_90_test.bam	bin_91_test.bam	bin_92_test.bam	bin_93_test.bam	bin_94_test.bam	bin_95_test.bam	bin_96_test.bam	bin_97_test.bam	bin_98_test.bam	bin_99_test.bam	bin_100_test.bam
ENSEMBL	chrM(+):1-2577	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0

This isn't correct. This script is setting the start position to -199 (1 - 200) and isn't respecting the chromosome boundary. So samtools view fails and doesn't return reads since the region isn't valid.

[charlesylin]

Thanks for flagging this. This code isn't actively maintained anymore, but this seems like a good edge case to flag. As you pointed out, the code will break in binning the regions and going outside of the chromatin regions. The error is upstream in the code when it's trying to segment the region and not with the getRawReads function. There should be a window parameter that's trying to expand the search region by 200 and that's why you're getting -199. Likewise, the code doesn't know the chromosome boundaries so it will extend it in either direction. You could try setting the window parameter to 0 and changing the number of bins. Easiest way to debug is to track the actual samtools view commands that it's trying to run. Best of luck,

…

-Charles Charles Y. Lin

On Fri, Aug 22, 2025 at 11:00 AM Andrew Thrasher ***@***.***> wrote: *adthrasher* created an issue (BradnerLab/pipeline#83) <#83> https://github.com/BradnerLab/pipeline/blob/8108e90f9adf7b403162eca5a7fb334fd8a5bed0/utils.py#L1115 All of these shell-outs need to check the return status of the command. For example running with the following feature: chrM ENSEMBL transcript 1 2577 . + . transcript_id=ENST00000387314.1 Yields all 0s in the coverage bins. GENE_ID locusLine bin_1_test.bam bin_2_test.bam bin_3_test.bam bin_4_test.bam bin_5_test.bam bin_6_test.bam bin_7_test.bam bin_8_test.bam bin_9_test.bam bin_10_test.bam bin_11_test.bam bin_12_test.bam bin_13_test.bam bin_14_test.bam bin_15_test.bam bin_16_test.bam bin_17_test.bam bin_18_test.bam bin_19_test.bam bin_20_test.bam bin_21_test.bam bin_22_test.bam bin_23_test.bam bin_24_test.bam bin_25_test.bam bin_26_test.bam bin_27_test.bam bin_28_test.bam bin_29_test.bam bin_30_test.bam bin_31_test.bam bin_32_test.bam bin_33_test.bam bin_34_test.bam bin_35_test.bam bin_36_test.bam bin_37_test.bam bin_38_test.bam bin_39_test.bam bin_40_test.bam bin_41_test.bam bin_42_test.bam bin_43_test.bam bin_44_test.bam bin_45_test.bam bin_46_test.bam bin_47_test.bam bin_48_test.bam bin_49_test.bam bin_50_test.bam bin_51_test.bam bin_52_test.bam bin_53_test.bam bin_54_test.bam bin_55_test.bam bin_56_test.bam bin_57_test.bam bin_58_test.bam bin_59_test.bam bin_60_test.bam bin_61_test.bam bin_62_test.bam bin_63_test.bam bin_64_test.bam bin_65_test.bam bin_66_test.bam bin_67_test.bam bin_68_test.bam bin_69_test.bam bin_70_test.bam bin_71_test.bam bin_72_test.bam bin_73_test.bam bin_74_test.bam bin_75_test.bam bin_76_test.bam bin_77_test.bam bin_78_test.bam bin_79_test.bam bin_80_test.bam bin_81_test.bam bin_82_test.bam bin_83_test.bam bin_84_test.bam bin_85_test.bam bin_86_test.bam bin_87_test.bam bin_88_test.bam bin_89_test.bam bin_90_test.bam bin_91_test.bam bin_92_test.bam bin_93_test.bam bin_94_test.bam bin_95_test.bam bin_96_test.bam bin_97_test.bam bin_98_test.bam bin_99_test.bam bin_100_test.bam ENSEMBL chrM(+):1-2577 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 This isn't correct. This script is setting the start position to -199 (1 - 200) and isn't respecting the chromosome boundary. So samtools view fails and doesn't return reads since the region isn't valid. — Reply to this email directly, view it on GitHub <#83>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABC4BL6D4QDF4GGAEJEINFD3O4V7NAVCNFSM6AAAAACESGSNJGVHI2DSMVQWIX3LMV43ASLTON2WKOZTGM2DKNZXGQYTGNA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[adthrasher]

Might I suggest archiving the repo so it is explicitly flagged as "unmaintained"? https://docs.github.com/en/repositories/archiving-a-github-repository/archiving-repositories