bamstats04 bug?

[ray1919]

Subject of the issue

bamstats could not find reads in certain region

Your environment

• version of jvarkit: recent
• version of java: 1.8
• the value of ${JAVA_HOME}
• which OS Ubuntu 16.04

Steps to reproduce

bamstats04 -B gene.bed.gz aligned.sorted.bam -o coverage.txt

most region in bed is calculated correctly, except one chr5 69509141 69509819 678 jss 0 0 0.0 0.0 678 0

there is a lot of reads in this region, like ST-E00310:553:HL3LWCCXY:5:1102:17523:43167 99 chr5 69509101 0 125M = 69509233 255 ST-E00310:553:HL3LWCCXY:5:1103:6076:3964 99 chr5 69509101 0 125M = 69509233 255 ST-E00310:553:HL3LWCCXY:5:1103:22536:8288 99 chr5 69509101 0 125M = 69509227 229 ST-E00310:553:HL3LWCCXY:5:1105:15666:2680 99 chr5 69509101 0 125M = 69509233 255 ST-E00310:553:HL3LWCCXY:5:1105:26595:9800 99 chr5 69509101 0 125M = 69509233 255 ST-E00310:553:HL3LWCCXY:5:1105:29508:70469 99 chr5 69509101 0 125M = 69509233 255 ST-E00310:553:HL3LWCCXY:5:1106:14072:5300 99 chr5 69509101 0 125M = 69509233 255 ST-E00310:553:HL3LWCCXY:5:1106:26971:14635 99 chr5 69509101 0 125M = 69509233 255 ST-E00310:553:HL3LWCCXY:5:1107:32491:44310 99 chr5 69509101 0 125M = 69509259 255 ST-E00310:553:HL3LWCCXY:5:1107:12033:62452 99 chr5 69509101 0 125M = 69509233 255

Expected behaviour

the result should not be 0. samtools depth gives right results.

Actual behaviour

most region in bed is calculated correctly, except one chr5 69509141 69509819 678 jss 0 0 0.0 0.0 678 0

[lindenb]

all those reads have MAPQ = 0

reads are not considered because MAPQ=0, if you want to use all the reads, specify --filter with an empty string:

 --filter ""

[ray1919]

Thank you for your prompt reply.